Dataset Information

Quantitative trait loci analysis of brown blotch resistance in cowpea variety KN1.

ABSTRACT: Cowpea is one of the most important crops in West Africa and is essential for the region's food and nutrition security and economic development. Consequently, improving its agronomic performance and yield is a desirable goal. Brown blotch disease, caused by the fungal pathogen Colletotrichum capsici, is an important constraint of cowpea productivity, and at present, only limited genetic resources are available for breeding improved brown blotch-resistant varieties. The current study has characterized the genetic basis for brown blotch resistance conferred by the cowpea cultivar KN1 and identified a major dominant quantitative trait locus (QTL) for resistance on chromosome Vu02. A segregating F₂ population (n?=?200), derived from a cross between KN1 and brown blotch-susceptible Tiligre (KVx775-33-2G), was developed and scored for disease severity following controlled inoculation. A subset of the population (n?=?94) was genotyped with 99 newly developed allele-specific polymerase chain reaction (AS-PCR) markers, and multiple interval mapping was performed. One major and three minor QTL were identified. This is the first reported mapping of QTL conferring resistance to C. capsici in cowpea, and it is expected that the markers identified here will be a valuable resource for developing elite cowpea cultivars with resistance to brown blotch.

SUBMITTER: Ohlson EW

PROVIDER: S-EPMC6096496 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Quantitative trait loci analysis of brown blotch resistance in cowpea variety KN1.

Ohlson Erik W EW Thio Gilles I GI Sawadogo Mahamadou M Sérémé Paco P Timko Michael P MP

Molecular breeding : new strategies in plant improvement 20180816 9

Cowpea is one of the most important crops in West Africa and is essential for the region's food and nutrition security and economic development. Consequently, improving its agronomic performance and yield is a desirable goal. Brown blotch disease, caused by the fungal pathogen <i>Colletotrichum capsici</i>, is an important constraint of cowpea productivity, and at present, only limited genetic resources are available for breeding improved brown blotch-resistant varieties. The current study has c ...[more]

PMID: 30147431

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Project description:BACKGROUND:Little is known about the genetic architecture of economically important traits in Brown Swiss cattle because only few genome-wide association studies (GWAS) have been carried out in this breed. Moreover, most GWAS have been performed for single traits, thus not providing detailed insights into potentially existing pleiotropic effects of trait-associated loci. RESULTS:To compile a comprehensive catalogue of large-effect quantitative trait loci (QTL) segregating in Brown Swiss cattle, we carried out association tests between partially imputed genotypes at 598,016 SNPs and daughter-derived phenotypes for more than 50 economically important traits, including milk production, growth and carcass quality, body conformation, reproduction and calving traits in 4578 artificial insemination bulls from two cohorts of Brown Swiss cattle (Austrian-German and Swiss populations). Across-cohort multi-trait meta-analyses of the results from the single-trait GWAS revealed 25 quantitative trait loci (QTL; P?<?8.36?×?10-?8) for economically relevant traits on 17 Bos taurus autosomes (BTA). Evidence of pleiotropy was detected at five QTL located on BTA5, 6, 17, 21 and 25. Of these, two QTL at BTA6:90,486,780 and BTA25:1,455,150 affect a diverse range of economically important traits, including traits related to body conformation, calving, longevity and milking speed. Furthermore, the QTL at BTA6:90,486,780 seems to be a target of ongoing selection as evidenced by an integrated haplotype score of 2.49 and significant changes in allele frequency over the past 25?years, whereas either no or only weak evidence of selection was detected at all other QTL. CONCLUSIONS:Our findings provide a comprehensive overview of QTL segregating in Brown Swiss cattle. Detected QTL explain between 2 and 10% of the variation in the estimated breeding values and thus may be considered as the most important QTL segregating in the Brown Swiss cattle breed. Multi-trait association testing boosts the power to detect pleiotropic QTL and assesses the full spectrum of phenotypes that are affected by trait-associated variants.

Project description:Genetic dissection of the S rat genome has provided strong evidence for the presence of two interacting blood pressure (BP) quantitative trait loci (QTLs), termed QTL1 and QTL2, on rat chromosome 5. However, the identities of the underlying interacting genetic factors remain unknown. Further experiments targeted to identify the interacting genetic factors by the substitution mapping approach alone are difficult because of the interdependency of natural recombinations to occur at the two QTLs. We hypothesized that the interacting genetic factors underlying these two QTLs may interact at the level of gene transcription and thereby represent expression QTLs (eQTLs). To detect these interacting eQTLs, a custom QTL chip containing the annotated genes within QTL1 and QTL2 was developed and used to conduct a transcriptional profiling study of S and two congenic strains that retain either one or both the QTLs. The results uncovered an interaction between two transcription factors, DMRTA2 and NFIA. Further, the âbiological signatureâ elicited by these two transcription factors was differential between the congenic strain that retained LEW alleles at both QTL1 and 2 compared to the congenic strain that retained LEW alleles at QTL1 alone. A network of transcription factors potentially affecting BP could be traced, lending support to our hypothesis. Pairs of Cy5 and Cy3 labeled targets were co-hybridized onto either a custom long oligonucleotide microarray for the interrogation of 231 genes encompassed by QTL1 and QTL2, or a TIGR rat cDNA array consisting of 26,401 probe elements representing 20,465 unique non-QTL genes. A âflip-dyeâ or âbalanced blockâ design was used as the experimental method of choice to account for potential dye-bias labeling effects. Six âbalanced blockâ normalized files are submitted for the long oligonucleotide array interrogating the hearts from S versus S.LEW(5)x6x9 animals, fourteen âflip-dyeâ hybridizations are submitted for the cDNA array interrogating the hearts from S versus S.LEW(5)x6x9 animals, and twelve âflip-dyeâ hybridizations are submitted for the cDNA array interrogating the hearts from S versus S.LEW(5)x6x11 animals. GPR and MEV files cannot be located.

Dataset Information

Quantitative trait loci analysis of brown blotch resistance in cowpea variety KN1.

Publications

Quantitative trait loci analysis of brown blotch resistance in cowpea variety KN1.

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