Combining disease resistance and postharvest quality traits by early marker-assisted backcrossing in carioca beans

Common bean is a worldwide important crop. The development of varieties with durable resistance to diseases is a major challenge in common bean breeding. The present study aimed at evaluating the phenotypic and molecular selection of anthracnose resistance in a population obtained by assisted backcrossing from IAC Formoso (resistant, donor parent) × BRS Pérola (susceptible, recurrent parent). Nine microsatellites (SSRs) and one Sequence Tagged Sites (STS) markers previously linked to ANT resistance were used to genotype this progeny, and the results showed that the selection of the genotypes closest to the donor parent in the BC1F1 population decreased the number of backcrossing cycles necessary to obtain advanced isogenic lines, potentiating the use of this tool for early selection of resistant cultivars. A total of 31 % of the BC1F1 progeny was selected and backcrossed again. The progeny derived from the second backcross (BC2F3) was selected for the Carioca grain ideotype, and 42 % of the genotypes showed high resistance to anthracnose under controlled conditions of infection for races 65 and 81. Superior resistant plants were selected and evaluated under natural conditions of infection to fusarium wilt and angular leaf spot, allowing the selection of two inbred lines with higher resistance to anthracnose, fusarium wilt, angular leaf spot and postharvest quality traits such as yield, 100 seed weight, L value at seed harvest grain darkening and cooking time. The approach outlined in this paper proved to be effective to simultaneously select for disease resistance without losing technological quality aspects of the bean.

Combining disease resistance and postharvest quality traits by early marker-assisted backcrossing in carioca beans

Common bean is a worldwide important crop. The development of varieties with durable resistance to diseases is a major challenge in common bean breeding. The present study aimed at evaluating the phenotypic and molecular selection of anthracnose resistance in a population obtained by assisted backcrossing from IAC Formoso (resistant, donor parent) × BRS Pérola (susceptible, recurrent parent). Nine microsatellites (SSRs) and one Sequence Tagged Sites (STS) markers previously linked to ANT resistance were used to genotype this progeny, and the results showed that the selection of the genotypes closest to the donor parent in the BC1F1 population decreased the number of backcrossing cycles necessary to obtain advanced isogenic lines, potentiating the use of this tool for early selection of resistant cultivars. A total of 31 % of the BC1F1 progeny was selected and backcrossed again. The progeny derived from the second backcross (BC2F3) was selected for the Carioca grain ideotype, and 42 % of the genotypes showed high resistance to anthracnose under controlled conditions of infection for races 65 and 81. Superior resistant plants were selected and evaluated under natural conditions of infection to fusarium wilt and angular leaf spot, allowing the selection of two inbred lines with higher resistance to anthracnose, fusarium wilt, angular leaf spot and postharvest quality traits such as yield, 100 seed weight, L value at seed harvest grain darkening and cooking time. The approach outlined in this paper proved to be effective to simultaneously select for disease resistance without losing technological quality aspects of the bean.

Genome-wide association mapping for heading date in oats under subtropical environments

Selection for heading date has been a decisive factor to increase areas cropped with oats in Brazil. Although important to oat breeders, genomic regions controlling heading date have not been completely identified. The objective of this study was to identify genomic regions controlling oat heading date in subtropical environments. A set of 412 oat genotypes, developed from 1974 to 2015, was assessed for heading date in contrasting environments and genotyped using genotyping-by-sequencing (GBS). Phenotypic and genotypic data were used in single and multi-environment association models. Quantitative trait loci (QTL) associated to heading date were identified on oat consensus groups Mrg02, Mrg05, Mrg06, Mrg12, and Mrg21. Some of the findings confirmed the association of genomic regions with heading date, while others emerge as new candidate regions associated to the trait. The genomic regions identified on Mrg02 and Mrg12 were associated to Vernalization 3 (Vrn3), while the genomic region identified on Mrg21 is associated with Vernalization 1 (Vrn1). The Vrn1 region was detected in Londrina, an environment with reduced vernalization condition, and in the multi-environment model. The results reveal that some genotypes of the panel are responsive to vernalization, increasing the days to heading without this environmental stimulus. Our results provide important contribution for a better understanding of heading date in subtropical environments and a strong basis for marker-assisted selection in oats.

Combining disease resistance and postharvest quality traits by early marker-assisted backcrossing in carioca beans

ABSTRACT: Common bean is a worldwide important crop. The development of varieties with durable resistance to diseases is a major challenge in common bean breeding. The present study aimed at evaluating the phenotypic and molecular selection of anthracnose resistance in a population obtained by assisted backcrossing from IAC Formoso (resistant, donor parent) × BRS Pérola (susceptible, recurrent parent). Nine microsatellites (SSRs) and one Sequence Tagged Sites (STS) markers previously linked to ANT resistance were used to genotype this progeny, and the results showed that the selection of the genotypes closest to the donor parent in the BC1F1 population decreased the number of backcrossing cycles necessary to obtain advanced isogenic lines, potentiating the use of this tool for early selection of resistant cultivars. A total of 31 % of the BC1F1 progeny was selected and backcrossed again. The progeny derived from the second backcross (BC2F3) was selected for the Carioca grain ideotype, and 42 % of the genotypes showed high resistance to anthracnose under controlled conditions of infection for races 65 and 81. Superior resistant plants were selected and evaluated under natural conditions of infection to fusarium wilt and angular leaf spot, allowing the selection of two inbred lines with higher resistance to anthracnose, fusarium wilt, angular leaf spot and postharvest quality traits such as yield, 100 seed weight, L value at seed harvest grain darkening and cooking time. The approach outlined in this paper proved to be effective to simultaneously select for disease resistance without losing technological quality aspects of the bean.

Association mapping in common bean revealed regions associated with Anthracnose and Angular Leaf Spot resistance

Despite important biotic stresses to common bean, Anthracnose (ANT) and Angular Leaf Spot (ALS) can cause losses of up to 80 % and occur in more than 60 countries around the world. Genetic resistance is the most sustainable strategy to manage these diseases. Thus, we aimed to (1) identify new SNP markers associated with ALS and ANT resistance loci in elite common bean lines, and (2) provide a functional characterization of the DNA sequences containing the identified SNP markers. We evaluated 60 inbred lines, under field conditions, which represent the elite germplasm developed by the Embrapa common bean breeding program across 22 years, in terms of severity of the ALS and ANT. The lines were genotyped with 5,398 SNPs. Then, a Mixed Linear Model was run to determine the SNP-trait associations. We observed two-significant marker-trait associations reacting to ANT, both located on chromosome Pv-02. These markers explained 25 % of the phenotypic variation. For ALS, only one significant marker-trait association was observed, which is located in chromosome Pv-10 and explained 19 % of the phenotypic variation. These markers, along with others already used, will be useful to add or keep ANT and ALS resistance loci identified in this work in the new carioca and black seeded cultivars.

Association mapping in common bean revealed regions associated with Anthracnose and Angular Leaf Spot resistance

Despite important biotic stresses to common bean, Anthracnose (ANT) and Angular Leaf Spot (ALS) can cause losses of up to 80 % and occur in more than 60 countries around the world. Genetic resistance is the most sustainable strategy to manage these diseases. Thus, we aimed to (1) identify new SNP markers associated with ALS and ANT resistance loci in elite common bean lines, and (2) provide a functional characterization of the DNA sequences containing the identified SNP markers. We evaluated 60 inbred lines, under field conditions, which represent the elite germplasm developed by the Embrapa common bean breeding program across 22 years, in terms of severity of the ALS and ANT. The lines were genotyped with 5,398 SNPs. Then, a Mixed Linear Model was run to determine the SNP-trait associations. We observed two-significant marker-trait associations reacting to ANT, both located on chromosome Pv-02. These markers explained 25 % of the phenotypic variation. For ALS, only one significant marker-trait association was observed, which is located in chromosome Pv-10 and explained 19 % of the phenotypic variation. These markers, along with others already used, will be useful to add or keep ANT and ALS resistance loci identified in this work in the new carioca and black seeded cultivars.(AU)

QTLs for seedling traits under salinity stress in hexaploid wheat / Caracterização de QTLs por traços de sementes sob o estresse de salinidade em trigo Hexaploid

Soil salinity limits agricultural production and is a major obstacle for increasing crop yield. Common wheat is one of the most important crops with allohexaploid characteristic and a highly complex genome. QTL mapping is a useful way to identify genes for quantitative traits such as salinity tolerance in hexaploid wheat. In the present study, a hydroponic trial was carried out to identify quantitative trait loci (QTLs) associated with salinity tolerance of wheat under 150mM NaCl concentration using a recombinant inbred line population (Xiaoyan 54×Jing 411). Values of wheat seedling traits including maximum root length (MRL), root dry weight (RDW), shoot dry weight (SDW), total dry weight (TDW) and the ratio of TDW of wheat plants between salt stress and control (TDWR) were evaluated or calculated. A total of 19QTLs for five traits were detected through composite interval mapping method by using QTL Cartographer version 2.5 under normal and salt stress conditions. These QTLs distributed on 12 chromosomes explained the percentage of phenotypic variation by individual QTL varying from 7.9% to 19.0%. Among them, 11 and six QTLs were detected under normal and salt stress conditions, respectively and two QTLs were detected for TDWR. Some salt tolerance related loci may be pleiotropic. Chromosome 1A, 3A and 7A may harbor crucial candidate genes associated with wheat salt tolerance. Our results would be helpful for the marker assisted selection to breed wheat varieties with improved salt tolerance.(AU)

A salinidade do solo limita a produção agrícola. O trigo mole é uma das culturas mais importantes com característica allohexaploid e genoma altamente complexo. O mapeamento QTL é uma maneira muito útil de identificar genes para traços quantitativos, como a tolerância à salinidade em trigo hexaplóide. No presente estudo realizou-se um ensaio hidropónico para identificar locos de traços quantitativos (QTLs) associados à tolerância à salinidade do trigo sob concentração de NaCl 150 mM, usando uma população de linhagem consanguíneo recombinante (Xiaoyan 54 × Jing 411). Os valores dos traços de mudas de trigo, incluindo comprimento máximo da raiz (MRL), peso seco da raiz (RDW), ponha o peso seco (SDW), peso seco total (TDW) e a proporção das plantas de trigo TDW entre o estresse salgado e o controle (TDWR), foram avaliados ou calculados. Um total de 19QTLs para cinco traços foram detectados através do método de mapeamento de intervalo composto usando a versão 2.5 do cartógrafo QTL sob condições normais e de estresse salino. Estes QTLs distribuídos em 12 cromossomos explicaram a porcentagem de variação fenotípica por QTL individual variando de 7,9% a 19,0%. Entre eles, foram detectados 11 e 6 QTLs em condições de estresse normal e sal, respectivamente, e dois QTLs foram detectados para TDWR. Cromossoma 1A, 3A e 7A podem conter genes que são candidatos cruciais associados à tolerância ao sal de trigo. Nossos resultados seriam úteis para a seleção assistida por marcadores para produzir variedades de trigo com tolerância salina melhorada.(AU)

QTLs for seedling traits under salinity stress in hexaploid wheat / Caracterização de QTLs por traços de sementes sob o estresse de salinidade em trigo Hexaploid

Soil salinity limits agricultural production and is a major obstacle for increasing crop yield. Common wheat is one of the most important crops with allohexaploid characteristic and a highly complex genome. QTL mapping is a useful way to identify genes for quantitative traits such as salinity tolerance in hexaploid wheat. In the present study, a hydroponic trial was carried out to identify quantitative trait loci (QTLs) associated with salinity tolerance of wheat under 150mM NaCl concentration using a recombinant inbred line population (Xiaoyan 54×Jing 411). Values of wheat seedling traits including maximum root length (MRL), root dry weight (RDW), shoot dry weight (SDW), total dry weight (TDW) and the ratio of TDW of wheat plants between salt stress and control (TDWR) were evaluated or calculated. A total of 19QTLs for five traits were detected through composite interval mapping method by using QTL Cartographer version 2.5 under normal and salt stress conditions. These QTLs distributed on 12 chromosomes explained the percentage of phenotypic variation by individual QTL varying from 7.9% to 19.0%. Among them, 11 and six QTLs were detected under normal and salt stress conditions, respectively and two QTLs were detected for TDWR. Some salt tolerance related loci may be pleiotropic. Chromosome 1A, 3A and 7A may harbor crucial candidate genes associated with wheat salt tolerance. Our results would be helpful for the marker assisted selection to breed wheat varieties with improved salt tolerance.

A salinidade do solo limita a produção agrícola. O trigo mole é uma das culturas mais importantes com característica allohexaploid e genoma altamente complexo. O mapeamento QTL é uma maneira muito útil de identificar genes para traços quantitativos, como a tolerância à salinidade em trigo hexaplóide. No presente estudo realizou-se um ensaio hidropónico para identificar locos de traços quantitativos (QTLs) associados à tolerância à salinidade do trigo sob concentração de NaCl 150 mM, usando uma população de linhagem consanguíneo recombinante (Xiaoyan 54 × Jing 411). Os valores dos traços de mudas de trigo, incluindo comprimento máximo da raiz (MRL), peso seco da raiz (RDW), ponha o peso seco (SDW), peso seco total (TDW) e a proporção das plantas de trigo TDW entre o estresse salgado e o controle (TDWR), foram avaliados ou calculados. Um total de 19QTLs para cinco traços foram detectados através do método de mapeamento de intervalo composto usando a versão 2.5 do cartógrafo QTL sob condições normais e de estresse salino. Estes QTLs distribuídos em 12 cromossomos explicaram a porcentagem de variação fenotípica por QTL individual variando de 7,9% a 19,0%. Entre eles, foram detectados 11 e 6 QTLs em condições de estresse normal e sal, respectivamente, e dois QTLs foram detectados para TDWR. Cromossoma 1A, 3A e 7A podem conter genes que são candidatos cruciais associados à tolerância ao sal de trigo. Nossos resultados seriam úteis para a seleção assistida por marcadores para produzir variedades de trigo com tolerância salina melhorada.

Molecular identification and mapping of a novel stripe rust resistance gene in wheat resistance line CH5389 / Identificação e mapeamento de um novo gene de resistência a ferrugem linear na linhagem de trigo CH5389

Stripe rust, caused by Puccinia striiformis is one of the most destructive diseases of wheat worldwide. CH5389 is a wheat-Thinopyrum intermedium derived line conferring stripe rust resistance. Genetic analyses of seedlings of F2 populations and F2:3 families developed by crossing CH5389 and susceptible common wheat revealed that stripe rust resistance in CH5389 was controlled by a single dominant gene that was designated YrCH5389. Eight SSR and EST-PCR polymorphic markers on chromosome 3AL were identified in F2 population of CH5389/Taichung29. The YrCH5389 was flanked by EST marker BE405348 and SSR marker Xwmc388 on chromosome 3AL with genetic distances of 2.2 and 4.6 cM, respectively. Comparative genomic analysis demonstrated that the orthologous genomic region of YrCH5389 covered 990 kb in rice, 640 kb in Brachypodium, and 890 kb in sorghum. Based on the locations of the markers, the resistance gene was located to chromosome deletion bin 3AL-0.85-1.00. Because there are no officially named stripe rust resistance genes on the 3AL chromosome, the YrCH5389 should be designated as a new resistance gene. These linkage markers could be useful for marker-assisted selection in wheat resistance breeding.(AU)

A ferrugem linear causada por Puccinia striiformis é uma das doenças mais destrutivas do trigo no mundo. A linhagem CH5389 é derivada do cruzamento de trigo com Thinopyrum intermedium e confere resistência a ferrugem linear. Análises genéticas de indivíduos da população F2 e família F2:3 obtida a partir do cruzamento entre CH5389 e trigo comum suscetível revelaram que a resistência à ferrugem linear na linhagem CH5389 foi controlada por um único gene dominante, designado YrCH5389. Oito marcadores polimórficos SSR e EST-PCR no cromossomo 3AL foram identificados na população F2 de CH5389/Taichung29. O gene YrCH5389 foi delimitado pelos marcadores EST BE405348 e SSR Xwmc388 no cromossomo 3AL com distâncias genéticas de 2,2 e 4,6 cM, respectivamente. Análises genômicas comparativas demonstraram que regiões genômicas ortólogas do gene YrCH5389 compreendem 990 kb em arroz, 640 kb em braquipódio e 890 kb em sorgo. Com base nas localizações dos marcadores, o gene de resistência foi localizado no cromossomo 3AL-0.85-1.00. Como não há genes oficialmente nomeados de resistência à ferrugem linear no cromossomo 3AL, o YrCH5389 deve ser designado como um gene novo de resistência. Esses marcadores de ligação podem ser úteis para a seleção assistida de genótipos de trigo resistentes a ferrugem linear.(AU)

Molecular identification and mapping of a novel stripe rust resistance gene in wheat resistance line CH5389 / Identificação e mapeamento de um novo gene de resistência a ferrugem linear na linhagem de trigo CH5389

Stripe rust, caused by Puccinia striiformis is one of the most destructive diseases of wheat worldwide. CH5389 is a wheat-Thinopyrum intermedium derived line conferring stripe rust resistance. Genetic analyses of seedlings of F2 populations and F2:3 families developed by crossing CH5389 and susceptible common wheat revealed that stripe rust resistance in CH5389 was controlled by a single dominant gene that was designated YrCH5389. Eight SSR and EST-PCR polymorphic markers on chromosome 3AL were identified in F2 population of CH5389/Taichung29. The YrCH5389 was flanked by EST marker BE405348 and SSR marker Xwmc388 on chromosome 3AL with genetic distances of 2.2 and 4.6 cM, respectively. Comparative genomic analysis demonstrated that the orthologous genomic region of YrCH5389 covered 990 kb in rice, 640 kb in Brachypodium, and 890 kb in sorghum. Based on the locations of the markers, the resistance gene was located to chromosome deletion bin 3AL-0.85-1.00. Because there are no officially named stripe rust resistance genes on the 3AL chromosome, the YrCH5389 should be designated as a new resistance gene. These linkage markers could be useful for marker-assisted selection in wheat resistance breeding.

A ferrugem linear causada por Puccinia striiformis é uma das doenças mais destrutivas do trigo no mundo. A linhagem CH5389 é derivada do cruzamento de trigo com Thinopyrum intermedium e confere resistência a ferrugem linear. Análises genéticas de indivíduos da população F2 e família F2:3 obtida a partir do cruzamento entre CH5389 e trigo comum suscetível revelaram que a resistência à ferrugem linear na linhagem CH5389 foi controlada por um único gene dominante, designado YrCH5389. Oito marcadores polimórficos SSR e EST-PCR no cromossomo 3AL foram identificados na população F2 de CH5389/Taichung29. O gene YrCH5389 foi delimitado pelos marcadores EST BE405348 e SSR Xwmc388 no cromossomo 3AL com distâncias genéticas de 2,2 e 4,6 cM, respectivamente. Análises genômicas comparativas demonstraram que regiões genômicas ortólogas do gene YrCH5389 compreendem 990 kb em arroz, 640 kb em braquipódio e 890 kb em sorgo. Com base nas localizações dos marcadores, o gene de resistência foi localizado no cromossomo 3AL-0.85-1.00. Como não há genes oficialmente nomeados de resistência à ferrugem linear no cromossomo 3AL, o YrCH5389 deve ser designado como um gene novo de resistência. Esses marcadores de ligação podem ser úteis para a seleção assistida de genótipos de trigo resistentes a ferrugem linear.

Identification of the Er1 resistence gene and RNase S-alleles in Malus prunifolia var. ringo rootstock

Woolly apple aphid (WAA; Eriosoma lanigerum Hausm.) is a major insect pest that has significant economic impact on apple growers worldwide. Modern breeding technologies rely on several molecular tools to help breeders select genetic determinants for traits of interest. Consequently, there is a need for specific markers linked to the genes of interest. Apple scions and rootstocks have an additional barrier to the introduction of pest resistance genes due to the presence of self-incompatibility S-RNase alleles. The genetic characterization and early identification of these alleles can amplify the contribution of a breeding program to the selection of resistant genitors that are as compatible as possible. In this study, we identified the Er1 gene involved in the resistance to WAA in Malus prunifolia var. ringo, also known as Maruba Kaido rootstock, and we analyzed the inheritance pattern of the WAA resistance Er1 gene in a segregant population derived from Malus pumila M.9 and Maruba Kaido rootstocks. The self-incompatibility of S-RNase alleles S6S26 of Maruba Kaido were also identified along with their inheritance pattern. We also confirmed the identification of the S1S3 alleles in the M.9 rootstock. To the best of our knowledge, this is the first study to characterize WAA resistance and RNase S-alleles in Maruba Kaido. Furthermore, we discuss the potential use of the genetic markers for these genes and their potential impact on apple breeding programs.

Identification of the Er1 resistence gene and RNase S-alleles in Malus prunifolia var. ringo rootstock

Woolly apple aphid (WAA; Eriosoma lanigerum Hausm.) is a major insect pest that has significant economic impact on apple growers worldwide. Modern breeding technologies rely on several molecular tools to help breeders select genetic determinants for traits of interest. Consequently, there is a need for specific markers linked to the genes of interest. Apple scions and rootstocks have an additional barrier to the introduction of pest resistance genes due to the presence of self-incompatibility S-RNase alleles. The genetic characterization and early identification of these alleles can amplify the contribution of a breeding program to the selection of resistant genitors that are as compatible as possible. In this study, we identified the Er1 gene involved in the resistance to WAA in Malus prunifolia var. ringo, also known as Maruba Kaido rootstock, and we analyzed the inheritance pattern of the WAA resistance Er1 gene in a segregant population derived from Malus pumila M.9 and Maruba Kaido rootstocks. The self-incompatibility of S-RNase alleles S6S26 of Maruba Kaido were also identified along with their inheritance pattern. We also confirmed the identification of the S1S3 alleles in the M.9 rootstock. To the best of our knowledge, this is the first study to characterize WAA resistance and RNase S-alleles in Maruba Kaido. Furthermore, we discuss the potential use of the genetic markers for these genes and their potential impact on apple breeding programs.(AU)

Estudos genômicos para a prolificidade em cabras: uma revisão sistemática

As características reprodutivas são de assaz importância para o sistema de produção de caprinos. Dentre essas características, a aplicação da prolificidade pode aumentar o aumento o número de partos múltiplos por ano, a pressão de seleção, redução do intervalo de geração e ganho genético anual. A herdabilidade para essa característica em cabras varia de 0,08 a 0,18. Os estudos de GWAS visam detectar variantes em loci genômicos que estão associados às características complexas. Entretanto, poucos estudos genômicos têm sido realizados em caprinos. O objetivo da pesquisa foi realizar uma revisão sistemática visando elucidar os avanços dos estudos genômicos no âmbito da prolificidade em cabras. Foram escolhidas três bases de dados para essa revisão: SCOPUS (2007-2018), PubMed (2008-2018) e BIOMED CENTRAL (2008-2018). Após os trabalhos de revisão, foram identificados 70 artigos de acordo com os seguintes critérios de busca: genomic ou GWAS, reproduction, animal, prolificacy e goat. Dentre eles excluíram-se 4 artigos repetidos, 41 cujos títulos possuíam conteúdo fora da área de estudo proposta, 20 abstracts relatando contexto divergente dessa pesquisa e 3 artigos de texto completo fora do âmbito estudado. Apenas dois artigos atenderam todos os critérios de elegibilidade, e foram elencados como objetos desse estudo. O artigo intitulado Whole-Genome Scanning for the Litter Size Trait Associated Genes and SNPs Under Selection in Dairy Goat (Capra hircus) utilizando-se dois grupos de cabras da raça Laoshan (alta fertilidade e baixa fertilidade), relataram a existência de genes candidatos relacionados à reprodução. Os genes CCNB2, AR, ADCY1, DNMT3B, SMAD2, AMHR2, ERBB2, FGFR1, MAP3K12 e THEM4 foram especificados para o grupo de cabras de alta fertilidade. Enquanto que KDM6A, TENM1, SWI5 e CYM, foram registrados no grupo de baixa fertilidade. Os genes SYCP2, SOX5 e POU3F4 foram localizados nos dois grupos. O segundo artigo aceito pelos critérios descritos Genetic Improvement of Litter Size in Four Goat Breeds in Egypt Using Polymorphism in Bone Morphogenetic Protein 15 Gene objetivou uma investigação do polimorfismo do gene BMP15 utilizando as técnicas PCR-RFLP e SNP em quatro raças de cabras no Egito e sua associação com a prolificidade. Os resultados mostraram a existência de sete SNPs, sendo quatro SNPs para alta prolificidade (760 G>C, 757 A>C, 762 G>A, e 769 G>C) e três SNPs para a baixa prolificidade. Os nucleotídeos codificantes de alta prolificidade apareceram em três raças (Alpina, Zaraibe e Baladi). O nucleotídeo de número 760 G>C mostrou presença em todas as cabras de alta prolificidade em todas as raças. Esses SNPs podem ser usados na MAS para melhorar essa característica nos rebanhos.

The reproductive traits are of importance for the goat production system. Among these characteristics, a prolific application to increase the number of multiple births per year, a selection pressure, reduction of production interval and annual genetic gain. The heritability for this characteristic in goats varies from 0.08 to 0.18. GWAS studies aim to detect variants in genomic loci that are associated with complex features. However, few genomic studies have been performed on goats. The objective of this research was to perform a systematic review to elucidate the advances of genomic studies in the field of goat proliferation. Three databases were selected for this review: SCOPUS (2007-2018), PubMed (2008- 2018) and BIOMED CENTRAL (2008-2018). After the review work, 70 articles were identified according to the following search criteria: genomic or GWAS, reproduction, animal, prolificacy and goat. Among them, 4 repeated articles were excluded, 41 whose titles had content outside the proposed study area, 20 abstracts reporting divergent context of this research and 3 full-text articles outside the scope studied. Only two articles met all eligibility criteria, and were listed as objects of this study. The article entitled Whole-Genome Scanning for the Litter Size Trait Associated Genes and SNPs Under Selection in Dairy Goat (Capra hircus) using two groups of Laoshan goats (high fertility and low fertility), reported the existence of candidate genes related to reproduction. The genes CCNB2, AR, ADCY1, DNMT3B, SMAD2, AMHR2, ERBB2, FGFR1, MAP3K12 and THEM4 were specified for the group of high fertility goats. While KDM6A, TENM1, SWI5 and CYM, were recorded in the low fertility group. The SYCP2, SOX5 and POU3F4 genes were located in both groups. The second article accepted by the criteria described Genetic Improvement of Litter Size in Four Goat Breeds in Egypt Using Polymorphism in Bone Morphogenetic Protein 15 Gene aimed to investigate the polymorphism of the BMP15 gene using PCRRFLP and SNP techniques in four goat breeds in Egypt and its association with prolificity. The results showed the existence of seven SNPs, four SNPs for high prolificacy (760 G> C, 757 A> C, 762 G> A, and 769 G> C) and three SNPs for low prolificity. High prolificity coding nucleotides appeared in three breeds (Alpina, Zaraibe and Baladi). The nucleotide number 760 G> C showed presence in all goats of high prolificacy in all breeds. These SNPs can be used in MAS to improve this trait in herds.

Application of molecular markers on genetic improvement and reproduction in the post-genomic era: emerging biotechnologies and perspectives in livestock

Background: New challenges are rising in the animal protein market, and one of the main world challenges is to produce more in shorter time, with better quality and in a sustainable way. Brazil is the largest beef exporter in volume hence the factors affecting the beef meat chain are of major concern in country´s economy. An emerging class of biotechnological approaches, the molecular markers, is bringing new perspectives to face these challenges, particularly after the publication of the first complete livestock genome (bovine), which has triggered a massive initiative to put in practice the benefits of the so called the Post-Genomic Era. Review: This article aimed at showing the directions and insights in the application of molecular markers on livestock genetic improvement and reproduction as well at organizing the progress so far, pointing some perspectives of these emerging technologies in Brazilian ruminant production context. An overview on the nature of the main molecular markers explored in ruminant production is provided, which describes the molecular bases and detection approaches available for microsatellites (STR) and single nucleotide polymorphisms (SNP). A topic is dedicated to review the history of association studies between markers and important trait variation in livestock, showing the timeline starting on quantitative trait loci (QTL) identification using STR markers and ending in high resolution SNP panels to proceed whole genome scans for phenotype/genotype association. Also the article organizes this information to reveal how QTL prospection using STR could open ground to the feasibility of marker-assisted selection and why this approach is quickly being replaced by studies involving the application of genome-wide association using SNP research in a new concept called genomic selection. Conclusion: The world's scientific community is dedicating effort and resources to apply SNP information in livestock selection through the development of high density panels for genomic association studies, connecting molecular genetic data with phenotypes of economic interest. Once generated, this information can be used to take decisions in genetic improvement programs by selecting animals with the assistance of molecular markers.

SELEÇÃO GENÔMICA PARA CARACTERÍSTICAS DE CARCAÇA EM BOVINOS DA RAÇA NELORE

Características economicamente importantes, como as características de carcaça, medidas post mortem, não vem sendo incluídas nos programas de melhoramento da raça Nelore devido, dentre outros fatores, aos altos custos e dificuldade de mensuração. Com a genômica, torna-se possível a seleção dos animais sem a necessidade de mensuração de seus próprios fenótipos e/ou de seus parentes, e tem-se, também, a possibilidadeda realização da buscapor genes ou regiões cromossômicas envolvidas com a expressão das características,por meio do estudo de associação genômica ampla (GWAS).Objetivou-se com o presente trabalho comparar diferentes modelosquanto à habilidade de predição de valores genéticos genômicos (GEBVs), e realizar um estudo de associação genômica ampla para as características: peso de carcaça quente, área de olho de lombo e espessura de gordura subcutânea, visando trazer subsídios paraa incorporação da informação genômica nas avaliações genéticas de bovinos de corte no Brasil.Foram utilizados dados fenotípicos e genotípicos de 1.756 animais machos da raça Nelore. Os animais foram genotipados com um painel de alta densidade com 777.962 SNPs. Os GEBVs foram preditos utilizando três modelos: Regressão de cumeeira (Bayesian Ridge Regression BRR), BayesC (BC) e Lasso Bayesiano (Bayesian Lasso - BL) e dois tipos de variáveis resposta: o valor genético tradicional e o fenótipo corrigido para os efeitos fixos.A implementação da GWAS foi realizada através da aplicação de um modelo poligênico-genômico, que considerou, simultaneamente, todasas informações disponíveis (fenótipos, pedigree e SNPs) por meio de um processo que combina a matriz de parentesco aditivo com a matriz de parentesco genômico.No geral, foi verificado que as predições genômicas sofreram influênciada herdabilidade das característicase do tipo de pseudo-fenótipo utilizado, sendo a medida fenotípica ajustada para os efeitos fixos a variável resposta mais adequada para se realizar as estimativas dos efeitos dos SNPs e GEBVs. Foi verificado, também, que os métodos BRR, BC e BL podem ser utilizados nas predições dos efeitos dos marcadores, obtendo-se, praticamente, a mesma acurácia de predição. No estudo de associação genômica ampla, foram identificadas algumas regiões cromossômicas polimórficas que podem estar associadas com a expressão das características analisadas. As regiões identificadas ajudam no entendimento do controle genético destas características e poderão contribuir para a inclusão das mesmas no processo de seleção dos animais. Os resultados do presente estudo mostraram quea seleção assistida por marcadorespode ser viável para a melhoria das características de carcaça em bovinos da raça Nelore.

Economic relevant traits as carcass, measured after slaughter,are not included in the animal breeding program of Nelore breed due to the difficult and high cost to measure. With the advent of genomic selection,it is possible to select animals without the need of recording phenotypic performance of its own or from close relatives, andthere isalso the possibility of investigatinggenes or chromosome regions affectingthe expression of traits using genome-wide association study (GWAS). The aim of this study was to compare different models on thepredictive ability of genomic breeding values (GEBVs), andto perform a GWAS for the following traits: hot carcass weight, rib eye area,andbackfat thickness, in orderto contribute to the incorporation of genomic information into the genetic evaluation of beef cattlein Brazil. Genotypic and phenotypic information of 1,756 Nelorebullswere used in the analysis. Genotypes were generated based on a panel with 777.962 SNPs. The GEBVs were predicted using three models: Bayesian Ridge Regression (BRR), BayesC (BC) e Bayesian Lasso (BL), and two types of response variables: estimated breeding value and adjusted phenotypes for the fixed effects. GWAS was performed using the single-step approach which combines all available phenotypic, pedigree and genomic informationadjusting apolygenic-genomic model. In general, it was verified that heritability and response variable affected the genomic predictions, where the adjusted phenotype was the most appropriate response variable to perform SNPs estimates. It was also observedthat the predictive abilities were similar among the methods (BRR, BC and BL). GWAS study detected potential genome regions that may be affecting the phenotypes. These regions can contribute to understand the genetic control of these traits and can be useful to include them into the genetic process for selecting the animals. The results showed that marker assited selection is feasible to improve carcass traits in Nelore cattle.

Loci de caracteres quantitativos (qtl) em peixes / Quantitative trait loci (qtl) in fishes / Loci de caracteres cuantitativos (qtl) en peces

Entre las aplicaciones del mapeo genómico está la búsqueda por loci de caracteres cuantitativos, influenciando características económicamente relevantes en la producción animal. La metodología identifica relaciones entre variaciones a nivel del ADN y valores fenotípicos. Esos datos fenotípicos pueden ser referentes a las características de herencia simple o cuantitativa (herencia poligénica). En años recientes, análisis han sido enfocadas, principalmente en caracteres cuantitativos, pues son la base de las características de producción. Sin embargo, la naturaleza poligénica de esos caracteres con variación continua dificulta análisis clásicos, que utiliza cruzamientos para aislamiento génico, principalmente en razón de la falta de segregación fenotípica discreta. En esos casos, regiones del ADN responsables por el fenotipo son definidas como QTL (Quantitative Trait Loci). Su identificación puede ser realizada por barredura genómica o por análisis individual de cromosomas. Un próximo paso es identificar los genes presentes en las regiones próximas a los marcadores unidos al QTL...(AU)

Among the applications of genome mapping is the search for loci that influence economically important quantitative traits in animal production. The methodology identifies the relationship among variations at DNA level and phenotypic values. These phenotypic data may be referent to traits of simple or quantitative (polygenic) inheritance. In recent years, analyses have been mainly focused in quantitative traits, since these are usually production traits. However, the polygenic nature of these particular characters with continuous variation makes it difficult to employ classical analyses of crosses for gene isolation, mainly due to the lack of discrete phenotypic segregation. In these cases, DNA regions responsible for the phenotype are defined as QTL (Quantitative Trait Loci). Its identification can be done by a whole-genome screening or analyzing chromosomes individually. A next step is to identify the genes present in the regions next to markers linked to QTL. The procedure is done by fine mapping, using a larger number of markers next to the region of the QTL position. This refinement of the linkage analysis or saturation of the mapping region allows reducing the size of the mapped region and thus reduce the number of possible genes related to the QTL...(AU)

Entre as aplicações do mapeamento genômico está a procura por loci de caracteres quantitativos, influenciando características economicamente importantes na produção animal. A metodologia identifica relações entre variações no nível do DNA e valores fenotípicos. Esses dados fenotípicos podem ser referentes à características de herança simples ou quantitativa (herança poligênica). Em anos recentes, análises têm sido focadas, principalmente em caracteres quantitativos, pois são a base das características de produção. No entanto, a natureza poligênica desses caracteres com variação contínua dificulta análises clássicas, por meio de cruzamento para isolamento gênico, principalmente em razão da falta de segregação fenotípica discreta. Nesses casos, regiões do DNA responsáveis pelo fenótipo são definidas como QTL (Quantitative Trait Loci). Sua identificação pode ser realizada por varredura genômica ou análise de cromossomos individualmente. Um próximo passo é identificar os genes presentes nas regiões próximas a marcadores ligados ao QTL. O procedimento é realizado por meio de mapeamento fino, com o emprego de um maior número de marcadores próximos a região de localização do QTL. Este refinamento da análise de ligação, ou saturação da região de mapeamento, permite reduzir o tamanho da região mapeada, e, portanto, reduzir o número de possíveis genes relacionados ao QTL...(AU)

Identification of molecular markers on bovine chromosome 18 associated to calving interval in a Brangus-Ibagé cattle herd / Identificação de marcadores moleculares no cromossomo bovino 18 associados ao intervalo entre partos em um rebanho Brangus-Ibagé

In the detection phase of a bovine marker assisted selection program, this paper investigated the genetic variability of three microsatellites on the chromosome 18 (BTA 18). The possible associations between genotypes or alleles of these markers versus weight at first calving and a lifetime calving interval (as indicators of reproductive performance) were evaluated in a beef cattle herd (5/8 Aberdeen Angus x 3/8 Nelore). Eleven alleles were detected in TGLA227 and ILSTS002 and three in BMS3004, the most frequent being TGLA227*79, ILSTS002*133, ILSTS002*135 and BMS3004*129. Polymorphic information content ranged from 0.41 to 0.84, while heterozygosity ranged from 49% to 86%, with an average value of 77%. The association analyses performed between genotype classes for the genetic markers versus weight at first calving indicated no significant result. Also, no correlation was observed between calving interval (CI) and TGLA227 genotypes. However, positive associations were detected between ILSTS002 and BMS3004 and CI. Animals carrying at least one ILSTS002*135 allele presented a CI about 39 days longer than the individuals with other genotypes; animals heterozygous for BMS3004 presented a CI about 35 days shorter than the homozygous. On these grounds, it can be concluded that these markers can be useful as an aid to fertility selection, in this herd.(AU)

Na fase de detecção, em um programa de seleção assistida por marcadores, em bovinos, este trabalho investigou a variabilidade genética de três microssatélites no cromossomo 18 (BTA 18). As possíveis associações entre genótipos ou alelos destes marcadores versus o peso ao primeiro parto e o intervalo entre partos (como indicadores do desempenho reprodutivo) foram avaliados em um rebanho de gado de corte (5/8 Aberdeen Angus x 3/8 Nelore). Onze alelos foram detectados em TGLA227 e ILSTS002 e três em BMS3004, os mais freqüentes sendo TGLA227*79, ILSTS002*133, ILSTS002*135 e BMS3004*129. O conteúdo polimórfico de informação variou de 0,41 a 0,84, enquanto a heterozigosidade variou de 49 a 86%, com média de 77%. As análises de associação efetuadas entre classes genotípicas dos marcadores genéticos versus o peso ao primeiro parto não indicaram resultados significantes. Da mesma forma, nenhuma correlação foi observada entre o intervalo entre partos (IEP) e os genótipos de TGLA227. Entretanto, associações positivas foram detectadas entre ILSTS002 e BMS3004 com o IEP. Animais portadores de pelo menos um alelo ILSTS002*135 apresentaram IEP cerca de 39 dias mais longo que os indivíduos com outros genótipos, e animais heterozigotos para BMS3004 apresentaram IEP cerca de 35 dias mais curto que os homozigotos. Assim, pode-se concluir que esses marcadores podem ser úteis como auxiliares na seleção para fertilidade, o rebanho em questão.(AU)

Diversity of microsatellites linked to the FSHbeta gene, their usefulness for individual identification and association with reproductive performance

The genetic diversity of three microsatellites (ILSTS027, MBO22, BM4325) mapped on the bovine chromosome 15 and linked to the follicle-stimulating hormone beta gene (FSHß) was investigated in cows of a Brangus Ibagé herd and the efficiency of these markers for individual identification and parentage control was estimated. Possible associations between each molecular marker and cow reproductive performance were also analyzed. Six alleles were detected in BM4325 and ILSTS027 and 12 in MB022, the most frequent being BM4325*101, BM4325*103, ILSTS027*169 and MB022*229. Polymorphic information content ranged from 0.58 to 0.88 while expected heterozygosity ranged from 65% to 89%, with an average mean value of 77%. Although only three markers were studied, the combined values indicate a high power of exclusion of a false parentage (94%) and of individual identification (3.8 x 10-4). The association analyses based on statistics parameters [MB022 (n=104, CI=545.3±127.0, WFC=349.9±53.4), BM4325 (n=106, CI=542.2±124.9, WFC=350.5±54.4) and ILSTS027 (n =105, CI=543.4 ± 124.5, WFC=350.1±54.5)] indicated no positive association between each microsatellite and weight at first calving. Calving interval (CI) also seemed not to be influenced by the ILSTS027 or MB022 system. However, carriers of at least one BM4325*101 allele presented a CI about 54 days shorter than the other animals (P=0.04; n=106). This marker could be useful for marker-assisted selection, allowing the improvement of reproductive performance, at least in the Brangus Ibagé herd.

A diversidade genética de três microssatélites (ILSTS027, MBO22, BM4325) mapeados no cromossomo bovino 15 e ligados ao gene do hormônio folículo estimulante, cadeia b (FSHbeta) foi investigada em fêmeas de um rebanho bovino Brangus Ibagé. Além de estimar a variabilidade genética do rebanho, avaliou-se a eficiência destes marcadores para a identificação individual e controle de paternidade. Verificaram-se também possíveis associações entre os marcadores e o desempenho reprodutivo. Seis alelos foram detectados em BM4325 e ILSTS027 e 12 foram observados em MB022, os mais freqüentes sendo, BM4325*101, BM4325*103, ILSTS027*169 e MB022*229. O conteúdo de informação polimórfica variou entre 0,58 a 0,88 enquanto a heterozigosidade esperada oscilou entre 65% e 89%, sendo o valor médio de 77%. Embora apenas três marcadores tenham sido investigados, os valores combinados indicam alto poder de exclusão de um falso progenitor (94%) e de identificação individual (3,8 x 10-4). As análises de associação baseadas nos parâmetros estatísticos [MB022 (n=104, CI=545,3±127,0, WFC=349,9±53,4), BM4325(n=106, CI=542,2±124,9, WFC=350,5±54,4) e ILSTS027(n=105, CI=543,4±124,5, WFC=350,1±54,5)] não indicaram associação positiva entre os microssatélites e o peso da vaca ao parto. O intervalo entre partos também não parece ser influenciado pelos marcadores ILSTS027 ou MB022. No entanto, portadores de pelo menos um alelo BM4325*101 apresentaram intervalo entre partos 54 dias mais curto que os demais animais (p=0,04; n=106). Este marcador pode ser útil para seleção assistida por marcadores, permitindo a melhoria do desempenho reprodutivo, pelo menos no rebanho Brangus Ibagé.

Diversity of microsatellites linked to the FSHbeta gene, their usefulness for individual identification and association with reproductive performance

The genetic diversity of three microsatellites (ILSTS027, MBO22, BM4325) mapped on the bovine chromosome 15 and linked to the follicle-stimulating hormone beta gene (FSHß) was investigated in cows of a Brangus Ibagé herd and the efficiency of these markers for individual identification and parentage control was estimated. Possible associations between each molecular marker and cow reproductive performance were also analyzed. Six alleles were detected in BM4325 and ILSTS027 and 12 in MB022, the most frequent being BM4325*101, BM4325*103, ILSTS027*169 and MB022*229. Polymorphic information content ranged from 0.58 to 0.88 while expected heterozygosity ranged from 65% to 89%, with an average mean value of 77%. Although only three markers were studied, the combined values indicate a high power of exclusion of a false parentage (94%) and of individual identification (3.8 x 10-4). The association analyses based on statistics parameters [MB022 (n=104, CI=545.3±127.0, WFC=349.9±53.4), BM4325 (n=106, CI=542.2±124.9, WFC=350.5±54.4) and ILSTS027 (n =105, CI=543.4 ± 124.5, WFC=350.1±54.5)] indicated no positive association between each microsatellite and weight at first calving. Calving interval (CI) also seemed not to be influenced by the ILSTS027 or MB022 system. However, carriers of at least one BM4325*101 allele presented a CI about 54 days shorter than the other animals (P=0.04; n=106). This marker could be useful for marker-assisted selection, allowing the improvement of reproductive performance, at least in the Brangus Ibagé herd.

A diversidade genética de três microssatélites (ILSTS027, MBO22, BM4325) mapeados no cromossomo bovino 15 e ligados ao gene do hormônio folículo estimulante, cadeia b (FSHbeta) foi investigada em fêmeas de um rebanho bovino Brangus Ibagé. Além de estimar a variabilidade genética do rebanho, avaliou-se a eficiência destes marcadores para a identificação individual e controle de paternidade. Verificaram-se também possíveis associações entre os marcadores e o desempenho reprodutivo. Seis alelos foram detectados em BM4325 e ILSTS027 e 12 foram observados em MB022, os mais freqüentes sendo, BM4325*101, BM4325*103, ILSTS027*169 e MB022*229. O conteúdo de informação polimórfica variou entre 0,58 a 0,88 enquanto a heterozigosidade esperada oscilou entre 65% e 89%, sendo o valor médio de 77%. Embora apenas três marcadores tenham sido investigados, os valores combinados indicam alto poder de exclusão de um falso progenitor (94%) e de identificação individual (3,8 x 10-4). As análises de associação baseadas nos parâmetros estatísticos [MB022 (n=104, CI=545,3±127,0, WFC=349,9±53,4), BM4325(n=106, CI=542,2±124,9, WFC=350,5±54,4) e ILSTS027(n=105, CI=543,4±124,5, WFC=350,1±54,5)] não indicaram associação positiva entre os microssatélites e o peso da vaca ao parto. O intervalo entre partos também não parece ser influenciado pelos marcadores ILSTS027 ou MB022. No entanto, portadores de pelo menos um alelo BM4325*101 apresentaram intervalo entre partos 54 dias mais curto que os demais animais (p=0,04; n=106). Este marcador pode ser útil para seleção assistida por marcadores, permitindo a melhoria do desempenho reprodutivo, pelo menos no rebanho Brangus Ibagé.

Introgression of bacterial leaf blight (BLB) resistant gene, Xa7 into MARDI elite variety, MR219 by marker assisted backcrossing (MABC) approach

Abstract Bacterial leaf blight (BLB) is one of the major rice diseases in Malaysia. This disease causes substantial yield loss as high as 70%. Development of rice varieties which inherited BLB resistant traits is a crucial approach to promote and sustain rice industry in Malaysia. Hence, this study aims were to enhance BLB disease resistant characters of high yielding commercial variety MR219 through backcross breeding approach with supporting tool of marker-assisted selection (MAS). Broad spectrum BLB resistance gene, Xa7 from donor parent IRBB7 were introgressed into the susceptible MR219 (recurrent parent) using two flanking markers ID7 and ID15. At BC3F4, we managed to generate 19 introgressed lines with homozygous Xa7 gene and showed resistant characteristics as donor parent when it was challenged with Xanthomonas oryzae pv. oryzae through artificial inoculation. Recurrent parent MR219 and control variety, MR263 were found to be severely infected by the disease. The improved lines exhibited similar morphological and yield performance characters as to the elite variety, MR219. Two lines, PB-2-107 and PB-2-34 were chosen to be potential lines because of their outstanding performances compared to parent, MR219. This study demonstrates a success story of MAS application in development of improved disease resistance lines of rice against BLB disease.

Resumo A mancha bacteriana das folhas (BLB) é uma das principais doenças do arroz na Malásia. Essa doença causa perdas substanciais de rendimento de até 70%. O desenvolvimento de variedades de arroz que herdaram características de resistência ao BLB é uma abordagem crucial para promover e sustentar a indústria do arroz na Malásia. Portanto, o objetivo deste estudo foi aumentar os caracteres BLB resistentes a doenças da variedade comercial MR219 de alto rendimento por meio de uma abordagem de cruzamento retrocruzamento com ferramenta de apoio de seleção assistida por marcador (MAS). O gene de resistência a BLB de amplo espectro, Xa7 do pai doador IRBB7, foi introgressado no MR219 suscetível (pai recorrente) usando dois marcadores flanqueadores ID7 e ID15. No BC3F4, conseguimos gerar 19 linhagens introgressadas com o gene Xa7 homozigoto e apresentamos características de resistência como genitor doador quando desafiado com Xanthomonas oryzae pv. oryzae por inoculação artificial. O pai recorrente MR219 e a variedade controle, MR263, estavam gravemente infectados pela doença. As linhas melhoradas exibiram características morfológicas e de desempenho de rendimento semelhantes às da variedade elite, MR219. Duas linhas, PB-2-107 e PB-2-34, foram escolhidas como linhas potenciais por causa de seus desempenhos excelentes em comparação com a mãe, MR219. Este estudo demonstra uma história de sucesso de aplicação de MAS no desenvolvimento de linhas de arroz melhoradas com resistência a doenças contra a doença BLB.