ABSTRACT
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.
Subject(s)
Oryza , Xanthomonas , Plant Diseases/genetics , Disease Resistance/genetics , Plant BreedingABSTRACT
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.
ABSTRACT
ABSTRACT One of the greatest challenges facing humanity is the development of sustainable strategies to ensure food availability in response to population growth and climate change. One approach that can contribute to increase food security is to close yield gaps and enhancing genetic gain; to such end, what is known as "molecular breeding" plays a fundamental role. Since a crop breeding program is mainly based on the quality of the germplasm, its detailed genetic characterization is mandatory to ensure the efficient use of genetic resources and accelerating development of superior varieties. Deep genotyping is an essential tool for a comprehensive characterization of the germplasm of interest and, fortunately, the technology is now accessible at a reasonable cost. What must be ensured is the correct interpretation of the genotypic information and on that basis develop efficient practical molecular crop breeding strategies that respond to the real needs of the breeding program.
RESUMEN Uno de los mayores desafíos que enfrenta la humanidad es el desarrollo de estrategias sostenibles para asegurar la disponibilidad de alimentos en respuesta al crecimiento de la población y el cambio climático. Un enfoque que puede contribuir a aumentar la seguridad alimentaria es cerrar las brechas de rendimiento y mejorar la ganancia genética; para tal fin, lo que se conoce como "mejoramiento molecular" juega un papel fundamental. Dado que un programa de mejoramiento de cultivos se basa principalmente en la calidad del germoplasma, su caracterización genética detallada es fundamental para garantizar el uso eficiente de los recursos genéticos y acelerar el desarrollo de variedades superiores. La genotipificación profunda es una herramienta esencial para una caracterización integral del germoplasma de interés y, afortunadamente, en la actualidad se puede acceder a la tecnología a un costo razonable. Lo que debe asegurarse es la interpretación correcta de la información genotípica y sobre esa base desarrollar estrategias eficientes y prácticas de mejoramiento molecular de cultivos que respondan a las necesidades reales del programa de mejoramiento.
ABSTRACT
This study aimed to validate the use of two SNP markers associated to a sdw1 allele identified previously in a short barley genotype (ND23049) with an adequate peduncle extrusion which reduces predisposition to fungal disease development. First, the GBS SNP were converted in a KASP marker but only one of them, named TP4712, correctly amplified all allelic variations and had a Mendelian segregation in a F2 population. To corroborate the association between TP4712 allele with plant height and peduncle extrusion, a total of 1221 genotypes were genotyped and evaluated for both traits. Out of the 1221 genotypes, 199 were F4 lines, 79 were a diverse panel, and 943 were two complete breeding cohorts of stage 1 yield trials. To corroborate the association between the sdw1 allele and the short plant height with adequate peduncle extrusion, contingency tables were created, grouping the 2427 data points into categories. Based on the contingency analysis, it was demonstrated that the higher proportion of short plants with adequate peduncle extrusion were present in genotypes carrying the SNP allele of ND23049 regardless the population and the sowing date. This study develops a marker-assisted selection tool to accelerate the introgression of favourable alleles for plant height and peduncle extrusion in adapted germplasm. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01371-7.
ABSTRACT
Bean leaf crumple virus (BLCrV) is a novel begomovirus (family Geminiviridae, genus Begomovirus) infecting common bean (Phaseolus vulgaris L.), threatening bean production in Latin America. Genetic resistance is required to ensure yield stability and reduce the use of insecticides, yet the available resistance sources are limited. In this study, three common bean populations containing a total of 558 genotypes were evaluated in different yield and BLCrV resistance trials under natural infection in the field. A genome-wide association study identified the locus BLC7.1 on chromosome Pv07 at 3.31 Mbp, explaining 8 to 16% of the phenotypic variation for BLCrV resistance. In comparison, whole-genome regression models explained 51 to 78% of the variation and identified the same region on Pv07 to confer resistance. The most significantly associated markers were located within the gene model Phvul.007G040400, which encodes a leucine-rich repeat receptor-like kinase subfamily III member and is likely to be involved in the innate immune response against the virus. The allelic diversity within this gene revealed five different haplotype groups, one of which was significantly associated with BLCrV resistance. As the same genome region was previously reported to be associated with resistance against other geminiviruses affecting common bean, our study highlights the role of previous breeding efforts for virus resistance in the accumulation of positive alleles against newly emerging viruses. In addition, we provide novel diagnostic single-nucleotide polymorphism markers for marker-assisted selection to exploit BLC7.1 for breeding against geminivirus diseases in one of the most important food crops worldwide.
Subject(s)
Genome-Wide Association Study , Phaseolus , Disease Resistance/genetics , Plant Breeding , Genotype , Phaseolus/genetics , Plant Leaves , Plant Diseases/geneticsABSTRACT
Tenderness is one of the main characteristics of meat because it determines its price and acceptability. This is the first bibliometric study on the trend of research on the role of genes in meat tenderness. A total of 175 original and English-language articles published up to 2021 were retrieved from Scopus. The bibliometric analysis was carried out with VOSviewer (version 1.6.18, Eck and Waltman, Leiden, Netherlands) and complemented with the Analyze search results service from Scopus. Erroneous and duplicate data were eliminated, and incomplete information was added to standardize the results. Scientific production was evaluated by means of quantity, quality and structure indicators. As a first glance, 8.816% of authors have published more than 50% of papers mainly related to genes encoding the calpain (CAPN)-calpastatin (CAST) system and single nucleotide polymorphisms (SNPs). Among other findings, a strong link was found between the contribution of the main countries (led by the United States with) and their institutions (led by the USDA Agricultural Research Service with) to their gross domestic product. Most studies on the topic are published in the Journal of Animal Science, and other journals with high impact according to the number of citations and different metrics. Finally, when evaluating the most cited articles, the occurrence and association of the main keywords, it was confirmed that research is focused on the role of CAPN and CAST genes and of SNPs in beef tenderness. The change in science was emphasized; although marker-assisted selection is still used, genes have an infinitesimal effect on complex traits. Therefore, since about 2010, new research groups adopted genomic selection to evaluate dense panels of SNPs and better explain genetic variation in meat tenderness.
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.
Subject(s)
Colletotrichum/pathogenicity , Phaseolus/genetics , Microsatellite Repeats/genetics , Disease ResistanceABSTRACT
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.
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.
Subject(s)
Phaseolus/genetics , Inbreeding , Microsatellite Repeats , FusariumABSTRACT
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.
Subject(s)
Avena/genetics , Flowers , Quantitative Trait Loci , Genome, Plant/geneticsABSTRACT
Leaf rust is one of the most significant diseases of wheat worldwide. In Argentina, it is one of the main reasons for variety replacement that becomes susceptible after large-scale use. Some varieties showed durable resistance to this disease, including Buck Manantial and Sinvalocho MA. RILs (Recombinant Inbred Lines) were developed for each of these varieties and used in genetics studies to identify components of resistance, both in greenhouse inoculations using leaf rust races, and in field evaluations under natural population infections. In Buck Manantial, the APR gene LrBMP1 was associated with resistance in field tests. In crosses involving Sinvalocho MA, four genes were previously identified and associated with resistance in field testing: APR (Adult Plant Resistance) gene LrSV1, the APR genetic system LrSV2 + LrcSV2 and the ASR (All Stage Resistance) gene LrG6. Using backcrosses, LrBMP1 was introgressed in four commercial susceptible varieties and LrSV1, LrSV2 + LrcSV2 and LrG6 were simultaneously introgressed in three susceptible commercial varieties. The use of molecular markers for recurrent parent background selection allowed us to select resistant lines with more than 80% similarity to commercial varieties. Additionally, progress towards positional cloning of the genetic system LrSV2 + LrcSV2 for leaf rust APR is reported.
ABSTRACT
The world population is expected to be larger and wealthier over the next few decades and will require more animal products, such as milk and beef. Tropical regions have great potential to meet this growing global demand, where pasturelands play a major role in supporting increased animal production. Better forage is required in consonance with improved sustainability as the planted area should not increase and larger areas cultivated with one or a few forage species should be avoided. Although, conventional tropical forage breeding has successfully released well-adapted and high-yielding cultivars over the last few decades, genetic gains from these programs have been low in view of the growing food demand worldwide. To guarantee their future impact on livestock production, breeding programs should leverage genotyping, phenotyping, and envirotyping strategies to increase genetic gains. Genomic selection (GS) and genome-wide association studies play a primary role in this process, with the advantage of increasing genetic gain due to greater selection accuracy, reduced cycle time, and increased number of individuals that can be evaluated. This strategy provides solutions to bottlenecks faced by conventional breeding methods, including long breeding cycles and difficulties to evaluate complex traits. Initial results from implementing GS in tropical forage grasses (TFGs) are promising with notable improvements over phenotypic selection alone. However, the practical impact of GS in TFG breeding programs remains unclear. The development of appropriately sized training populations is essential for the evaluation and validation of selection markers based on estimated breeding values. Large panels of single-nucleotide polymorphism markers in different tropical forage species are required for multiple application targets at a reduced cost. In this context, this review highlights the current challenges, achievements, availability, and development of genomic resources and statistical methods for the implementation of GS in TFGs. Additionally, the prediction accuracies from recent experiments and the potential to harness diversity from genebanks are discussed. Although, GS in TFGs is still incipient, the advances in genomic tools and statistical models will speed up its implementation in the foreseeable future. All TFG breeding programs should be prepared for these changes.
ABSTRACT
Persistency is the rate of decrease after milk production peak, mathematical models such as Wood's can be used to estimate it for describing the lactation curve and its rate of descent; random regression models are also useful, as they describe the genetic lactation curve for each animal. The objective of this study was to compare Best Linear Unbiased Prediction (BLUP), marker-assisted BLUP (MBLUP) model and random regression model (RRM) to estimate genetic parameters and breeding values for the lactation persistency curve. 4,658 test day measurements were available for 733 individuals, from which lactation curves were described to calculate persistency, estimating genetic parameters and values for this trait through BLUP and MBLUP. A similar process was done for RRM, where persistency was estimated from the genetic lactation curve. The heritability obtained using RRM was 0.51, greater than that obtained by BLUP (0.29) and MBLUP (0.21). The reliability of the genetic value for persistency in bulls was greater when RRM was used, but there was no correlation between the genetic values of different models. The highest heritability for persistency and the more reliable genetic values for bulls were achieved under the RRM, it allows positioning this methodology as an important tool for genetic evaluation of persistency.
Subject(s)
Lactation , Milk , Animals , Cattle/genetics , Female , Male , Models, Genetic , Phenotype , Reproducibility of ResultsABSTRACT
BACKGROUND: Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using a transcriptomic approach, in order to identify and characterize SNP and InDel markers associated with berry size in table grapes. We used an integrative analysis based on RNA-Seq, SNP/InDel search and validation on table grape segregants and varieties with different genetic backgrounds. RESULTS: Thirty SNPs and eight InDels were identified using a transcriptomic approach (RNA-Seq). These markers were selected from SNP/InDel found among segregants from a Ruby x Sultanina population with contrasting phenotypes for berry size. The set of 38 SNP and InDel markers was distributed in eight chromosomes. Genotype-phenotype association analyses were performed using a set of 13 RxS segregants and 41 table grapes varieties with different genetic backgrounds during three seasons. The results showed several degrees of association of these markers with berry size (10.2 to 30.7%) as other berry-related traits such as length and width. The co-localization of SNP and /or InDel markers and previously reported QTLs and candidate genes associated with berry size were analysed. CONCLUSIONS: We identified a set of informative and transferable SNP and InDel markers associated with berry size. Our results suggest the suitability of SNPs and InDels as candidate markers for berry weight in seedless table grape breeding. The identification of genomic regions associated with berry weight in chromosomes 8, 15 and 17 was achieved with supporting evidence derived from a transcriptome experiment focused on SNP/InDel search, as well as from a QTL-linkage mapping approach. New regions possibly associated with berry weight in chromosomes 3, 6, 9 and 14 were identified.
Subject(s)
Fruit/genetics , INDEL Mutation , Polymorphism, Single Nucleotide , Vitis/genetics , Fruit/growth & development , Gene Expression Profiling , Genetic Markers , Genotype , Phenotype , Quantitative Trait Loci , RNA, Plant , RNA-Seq , Vitis/growth & developmentABSTRACT
BACKGROUND: Wheat is one of the most important crops cultivated all over the world. New high-yielding cultivars that are more resistant to fungal diseases have been permanently developed. The present study aimed at the possibility of accelerating the process of breeding new cultivars, resistant to eyespot, by using doubled haploids (DH) system supported by marker-assisted selection. RESULTS: Two highly resistant breeding lines (KBP 0916 and KBH 4942/05) carrying Pch1 gene were crossed with the elite wheat genotypes. Hybrid plants of early generations were analyzed using endopeptidase EpD1 and two SSR markers linked to the Pch1 locus. Selected homozygous and heterozygous genotypes for the Pch1-linked EpD1b allele were used to produce haploid plants. Molecular analyses were performed on haploids to identify plants possessing Pch1 gene. Chromosome doubling was performed only on haploid plants with Pch1 gene. Finally, 65 DH lines carrying eyespot resistance gene Pch1 and 30 lines without this gene were chosen for the eyespot resistance phenotyping in a field experiment. CONCLUSIONS: Results of the experiment confirmed higher resistance to eyespot of the genotypes with Pch1 in comparison to those without this gene. This indicates the efficiency of selection at the haploid level.
Subject(s)
Selection, Genetic , Triticum/genetics , Triticum/metabolism , Haploidy , Plant Diseases , Breeding/methods , Gene Expression , Microsatellite Repeats , GenotypeABSTRACT
BACKGROUND: Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. RESULTS: We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. CONCLUSIONS: Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.
Subject(s)
Ascomycota/physiology , Chromosome Mapping , Disease Resistance/genetics , Genetic Loci/genetics , Glycine max/genetics , Plant Diseases/microbiology , Polymorphism, Single Nucleotide , Alleles , Genetic Markers/genetics , Phenotype , Plant Diseases/immunology , Glycine max/immunology , Glycine max/microbiologyABSTRACT
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.
ABSTRACT
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)
ABSTRACT
Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a SNP genotyping platform, a large SNP data set and a number of applications on how to utilize this information to improve the efficiency and quality of seed handling activities, breeding, and seed dissemination through molecular tools.