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1.
BMC Genomics ; 22(1): 267, 2021 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-33853519

RESUMO

BACKGROUND: The back plays a vital role in horse locomotion, where the spine functions as a spring during the stride cycle. A complex interaction between the spine and the muscles of the back contribute to locomotion soundness, gait ability, and performance of riding and racehorses. Conformation is commonly used to select horses for breeding and performance in multiple horse breeds, where the back and croup conformation plays a significant role. The conformation of back and croup plays an important role on riding ability in Icelandic horses. However, the genes behind this trait are still unknown. Therefore, the aim of this study was to identify genomic regions associated with conformation of back and croup in Icelandic horses and to investigate their effects on riding ability. One hundred seventy-seven assessed Icelandic horses were included in the study. A genome-wide association analysis was performed using the 670 K+ Axiom Equine Genotyping Array, and the effects of different haplotypes in the top associated region were estimated for riding ability and additional conformation traits assessed during breeding field tests. RESULTS: A suggestive quantitative trait loci (QTL) for the score of back and croup was detected on Equus caballus (ECA) 22 (p-value = 2.67 × 10- 7). Haplotype analysis revealed two opposite haplotypes, which resulted in higher and lower scores of the back and croup, respectively (p-value < 0.001). Horses with the favorable haplotype were more inclined to have a well-balanced backline with an uphill conformation and had, on average, higher scores for the lateral gaits tölt (p-value = 0.02) and pace (p-value = 0.004). This genomic region harbors three genes: C20orf85, ANKRD60 and LOC100056167. ANKRD60 is associated with body height in humans. C20orf85 and ANKRD60 are potentially linked to adolescent idiopathic scoliosis in humans. CONCLUSIONS: Our results show that the detected QTL for conformation of back and croup is of importance for quality of lateral gaits in Icelandic horses. These findings could result in a genetic test to aid in the selection of breeding horses, thus they are of major interest for horse breeders. The results may also offer a gateway to comparative functional genomics by potentially linking both motor laterality and back inclination in horses with scoliosis in humans.


Assuntos
Marcha , Cavalos/genética , Locos de Características Quantitativas , Animais , Marcha/genética , Estudo de Associação Genômica Ampla , Fenótipo
2.
J Exp Bot ; 71(3): 893-906, 2020 01 23.
Artigo em Inglês | MEDLINE | ID: mdl-31781747

RESUMO

Flowering time is a complex trait and has a key role in crop yield and adaptation to environmental stressors such as heat and drought. This study aimed to better understand the interconnected dynamics of epistasis and environment and look for novel regulators. We investigated 534 spring barley MAGIC DH lines for flowering time at various environments. Analysis of quantitative trait loci (QTLs), epistatic interactions, QTL × environment (Q×E) interactions, and epistasis × environment (E×E) interactions were performed with single SNP and haplotype approaches. In total, 18 QTLs and 2420 epistatic interactions were detected, including intervals harboring major genes such as Ppd-H1, Vrn-H1, Vrn-H3, and denso/sdw1. Epistatic interactions found in field and semi-controlled conditions were distinctive. Q×E and E×E interactions revealed that temperature influenced flowering time by triggering different interactions between known and newly detected regulators. A novel flowering-delaying QTL allele was identified on chromosome 1H (named 'HvHeading') and was shown to be engaged in epistatic and environment interactions. Results suggest that investigating epistasis, environment, and their interactions, rather than only single QTLs, is an effective approach for detecting novel regulators. We assume that barley can adapt flowering time to the environment via alternative routes within the pathway.


Assuntos
Epistasia Genética , Flores/crescimento & desenvolvimento , Interação Gene-Ambiente , Hordeum/crescimento & desenvolvimento , Locos de Características Quantitativas , Hordeum/genética
3.
Plant Dis ; 104(7): 1944-1948, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32384254

RESUMO

Southern corn rust (SCR) is a prevalent foliar disease that can lead to severe yield losses in maize. Growing SCR-resistant varieties is the most effective way to control the disease. To identify major quantitative trait loci (QTLs) for SCR resistance, a recombinant inbred line population derived from a cross between CIMBL83 (resistant) and Lx9801 (susceptible) was analyzed. The resistance to SCR had high heritability within the population, and a major QTL on chromosome 4 (qSCR4.01), which can explain 48 to 65% of the total phenotypic variation, was consistently detected across multiple environments. Using a progeny-based fine-mapping strategy, we delimited qSCR4.01 to an interval of ∼770 kb. In contrast to other major QTLs for SCR resistance previously reported on the short arm of chromosome 10, qSCR4.01 is a novel QTL and, therefore, a desirable source of SCR resistance in maize breeding programs.


Assuntos
Locos de Características Quantitativas , Zea mays/genética , Mapeamento Cromossômico , Resistência à Doença/genética , Humanos , Doenças das Plantas
4.
BMC Genomics ; 20(1): 891, 2019 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-31752676

RESUMO

BACKGROUND: Barley yellow dwarf (BYD) is an important virus disease that causes significant reductions in wheat yield. For effective control of Barley yellow dwarf virus through breeding, the identification of genetic sources of resistance is key to success. In this study, 335 geographically diverse wheat accessions genotyped using an Illumina iSelect 90 K single nucleotide polymorphisms (SNPs) bead chip array were used to identify new sources of resistance to BYD in different environments. RESULTS: A genome-wide association study (GWAS) performed using all the generalised and mixed linkage models (GLM and MLM, respectively) identified a total of 36 significant marker-trait associations, four of which were consistently detected in the K model. These four novel quantitative trait loci (QTL) were identified on chromosomes 2A, 2B, 6A and 7A and associated with markers IWA3520, IWB24938, WB69770 and IWB57703, respectively. These four QTL showed an additive effect with the average visual symptom score of the lines containing resistance alleles of all four QTL being much lower than those with less favorable alleles. Several Chinese landraces, such as H-205 (Baimazha) and H-014 (Dahongmai) which have all four favorable alleles, showed consistently higher resistance in different field trials. None of them contained the previously described Bdv2, Bdv3 or Bdv4 genes for BYD resistance. CONCLUSIONS: This study identified multiple novel QTL for BYD resistance and some resistant wheat genotypes. These will be useful for breeders to generate combinations with and/or without Bdv2 to achieve higher levels and more stable BYD resistance.


Assuntos
Resistência à Doença/genética , Luteovirus , Doenças das Plantas/genética , Doenças das Plantas/virologia , Triticum/genética , Triticum/virologia , Estudo de Associação Genômica Ampla , Locos de Características Quantitativas
6.
Chemosphere ; 317: 137885, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-36682639

RESUMO

Aluminum (Al) toxicity is a major threat to the productivity and quality of wheat on acid soil. Identifying novel Al tolerance genes is crucial for breeders to pyramid different tolerance mechanisms thus leading to greater Al tolerance. We aim to identify novel quantitative trait loci (QTL) and key candidate genes associated with Al tolerance in wheat. Herein, we investigated the genotypic variation in Al tolerance among 334 wheat varieties using an acid soil assay. Genome-wide association study (GWAS) and transcriptome were carried out to identify key genes for Al tolerance. GWAS identified several QTL associated with acid soil tolerance including one major QTL on chromosome 1A, in addition to the QTL on 4D where TaALMT1 is located. The four significant markers around the newly identified QTL explained 27.2% of the phenotypic variation. With the existence of reported markers for TaALMT1, more than 97% of the genotypes showed tolerance to Al. For those genotypes with the existence of the novel QTL on 1A but without TaALMT1, more than 90% of genotypes showed medium or high tolerance to Al, confirming the existence of the Al tolerance gene(s) on chromosome 1A. By combining GWAS and RNA-seq analysis, we identified 11 candidate genes associated with Al tolerance. The results provide new insights into the genetic basis of Al tolerance in wheat. The identified genes can be used for the breeding of Al tolerant accessions.


Assuntos
Estudo de Associação Genômica Ampla , Triticum , Mapeamento Cromossômico , Triticum/genética , Alumínio/toxicidade , Transcriptoma , Melhoramento Vegetal , Solo , Fenótipo
7.
Rice (N Y) ; 12(1): 63, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31410650

RESUMO

BACKGROUND: Salinity is one of the most widespread abiotic stresses affecting rice productivity worldwide. The purpose of this study was to establish the relative importance of different traits associated with salinity tolerance in rice and to identify new quantitative trait loci (QTL) conferring tolerance to salinity at seedling stage. A total of 231 F2:3 plants derived from a cross between a sensitive variety BRRI dhan29 (BR29 hereafter) and Capsule, a salt tolerant Bangladeshi indica landrace, were evaluated under salt stress in a phytotron. RESULTS: Out of the 231 F2 plants, 47 highly tolerant and 47 most sensitive lines were selected, representing the two extreme tails of the phenotypic distribution. These 94 plants were genotyped for 105 simple sequence repeat (SSR) and insertion/deletion (InDel) markers. A genetic linkage map spanning approximately 1442.9 cM of the 12 linkage groups with an average marker distance of 13.7 cM was constructed. QTL were identified on the long arm of chromosome 1 for Na+ concentration, K+ concentration, Na+-K+ ratio and survival; chromosome 3 for Na+ concentration, survival and overall phenotypic evaluation using the Standard Evaluation system (SES); and chromosome 5 for SES. A total of 6 pairwise epistatic interactions were also detected between QTL-linked and QTL-unlinked regions. Graphical genotyping indicated an association between the phenotypes of the extreme families and their QTL genotypes. Path coefficient analysis revealed that Na+ concentration, survival, Na+-K+ ratio and the overall phenotypic performance (SES score) are the major traits associated with salinity tolerance of Capsule. CONCLUSIONS: Capsule provides an alternative source of salinity tolerance aside from Pokkali and Nona Bokra, the two Indian salt tolerant landraces traditionally used for breeding salt tolerant rice varieties. Pyramiding the new QTL identified in this study with previously discovered loci, such as Saltol, will facilitate breeding varieties that are highly tolerant of salt stress.

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