Dataset Information

QTLs associated with agronomic traits in the Attila × CDC Go spring wheat population evaluated under conventional management.

ABSTRACT: Recently, we investigated the effect of the wheat 90K single nucleotide polymorphic (SNP) array and three gene-specific (Ppd-D1, Vrn-A1 and Rht-B1) markers on quantitative trait loci (QTL) detection in a recombinant inbred lines (RILs) population derived from a cross between two spring wheat (Triticum aestivum L.) cultivars, 'Attila' and 'CDC Go', and evaluated for eight agronomic traits at three environments under organic management. The objectives of the present study were to investigate the effect of conventional management on QTL detection in the same mapping population using the same set of markers as the organic management and compare the results with organic management. Here, we evaluated 167 RILs for number of tillers (tillering), flowering time, maturity, plant height, test weight (grain volume weight), 1000 kernel weight, grain yield, and grain protein content at seven conventionally managed environments from 2008 to 2014. Using inclusive composite interval mapping (ICIM) on phenotypic data averaged across seven environments and a subset of 1203 informative markers (1200 SNPs and 3 gene specific markers), we identified a total of 14 QTLs associated with flowering time (1), maturity (2), plant height (1), grain yield (1), test weight (2), kernel weight (4), tillering (1) and grain protein content (2). Each QTL individually explained from 6.1 to 18.4% of the phenotypic variance. Overall, the QTLs associated with each trait explained from 9.7 to 35.4% of the phenotypic and from 22.1 to 90.8% of the genetic variance. Three chromosomal regions on chromosomes 2D (61-66 cM), 4B (80-82 cM) and 5A (296-297 cM) harbored clusters of QTLs associated with two to three traits. The coincidental region on chromosome 5A harbored QTL clusters for both flowering and maturity time, and mapped about 2 cM proximal to the Vrn-A1 gene, which was in high linkage disequilibrium (0.70 ? r2 ? 0.75) with SNP markers that mapped within the QTL confidence interval. Six of the 14 QTLs (one for flowering time and plant height each, and two for maturity and kernel weight each) were common between the conventional and organic management systems, which suggests issues in directly utilizing gene discovery results based on conventional management to make in detail selection (decision) for organic management.

SUBMITTER: Zou J

PROVIDER: S-EPMC5291526 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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QTLs associated with agronomic traits in the Attila × CDC Go spring wheat population evaluated under conventional management.

Zou Jun J Semagn Kassa K Iqbal Muhammad M Chen Hua H Asif Mohammad M N'Diaye Amidou A Navabi Alireza A Perez-Lara Enid E Pozniak Curtis C Yang Rong-Cai RC Randhawa Harpinder H Spaner Dean D

PloS one 20170203 2

Recently, we investigated the effect of the wheat 90K single nucleotide polymorphic (SNP) array and three gene-specific (Ppd-D1, Vrn-A1 and Rht-B1) markers on quantitative trait loci (QTL) detection in a recombinant inbred lines (RILs) population derived from a cross between two spring wheat (Triticum aestivum L.) cultivars, 'Attila' and 'CDC Go', and evaluated for eight agronomic traits at three environments under organic management. The objectives of the present study were to investigate the e ...[more]

PMID: 28158253

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Project description:We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars 'Cutler' and 'AC Barrie' using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study using microsatellite and DArT markers. Results from this study provide additional information to wheat researchers developing early maturing and short stature spring wheat cultivars.

Project description:BackgroundWheat is a cool seasoned crop requiring low temperature during grain filling duration and therefore increased temperature causes significant yield reduction. A set of 125 spring wheat genotypes from International Maize and Wheat Improvement Centre (CIMMYT-Mexico) was evaluated for phenological and yield related traits at three locations in Pakistan under normal sowing time and late sowing time for expose to prolonged high temperature. With the help of genome-wide association study using genotyping-by-sequencing, marker trait associations (MTAs) were observed separately for the traits under normal and late sown conditions.ResultsSignificant reduction ranging from 9 to 74% was observed in all traits under high temperature. Especially 30, 25, 41 and 66% reduction was observed for days to heading (DH), plant height (PH), spikes per plant (SPP) and yield respectively. We identified 55,954 single nucleotide polymorphisms (SNPs) using genotyping by sequencing of these 125 hexaploid spring wheat genotypes and conducted genome-wide association studies (GWAS) for days to heading (DH), grain filled duration (GFD), plant height (PH), spikes per plant (SPP), grain number per spike (GNS), thousand kernel weight (TKW) and grain yield per plot (GY). Genomic regions identified through GWAS explained up to 13% of the phenotypic variance, on average. A total of 139 marker-trait associations (MTAs) across three wheat genomes (56 on genome A, 55 on B and 28 on D) were identified for all the seven traits studied. For days to heading, 20; grain filled duration, 21; plant height, 23; spikes per plant, 13; grain numbers per spike, 8; thousand kernel weight, 21 and for grain yield, 33 MTAs were detected under normal and late sown conditions.ConclusionsThis study identifies the essential resource of genetics research and underpins the chromosomal regions of seven agronomic traits under normal and high temperature. Significant relationship was observed between the number of favored alleles and trait observations. Fourteen protein coding genes with their respective annotations have been searched with the sequence of seven MTAs which were identified in this study. These findings will be helpful in the development of a breeder friendly platform for the selection of high yielding wheat lines at high temperature areas.

Project description:BackgroundSorghum is an important C4 crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization.ResultsA bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha(-1) fertilizer) and low N (0 kg.ha(-1) fertilizer) conditions. A linkage map spanning 1614 cM was developed using 642 polymorphic single nucleotide polymorphisms (SNPs) detected in the population using Genotyping-By-Sequencing (GBS) technology. Composite interval mapping detected a total of 38 QTLs for 11 agronomic traits tested under different nitrogen levels. The phenotypic variation explained by individual QTL ranged from 6.2 to 50.8%. Illumina RNA sequencing data generated on seedling root tissues revealed 726 differentially expressed gene (DEG) transcripts between parents, of which 108 were mapped close to the QTL regions.ConclusionsCo-localized regions affecting multiple traits were detected on chromosomes 1, 5, 6, 7 and 9. These potentially pleiotropic regions were coincident with the genomic regions of cloned QTLs, including genes associated with flowering time, Ma3 on chromosome 1 and Ma1 on chromosome 6, gene associated with plant height, Dw2 on chromosome 6. In these regions, RNA sequencing data showed differential expression of transcripts related to nitrogen metabolism (Ferredoxin-nitrate reductase), glycolysis (Phosphofructo-2-kinase), seed storage proteins, plant hormone metabolism and membrane transport. The differentially expressed transcripts underlying the pleiotropic QTL regions could be potential targets for improving sorghum performance under limited N fertilizer through marker assisted selection.

Dataset Information

QTLs associated with agronomic traits in the Attila × CDC Go spring wheat population evaluated under conventional management.

Publications

QTLs associated with agronomic traits in the Attila × CDC Go spring wheat population evaluated under conventional management.

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