Quantitative trait loci of acid detergent fiber and grain chemical composition in hulled × hull-less barley population

Abdel‐Haleem, Hussein; Bowman, J. G. P.; Giroux, Michael J.; Kanazin, Vladimir; Talbert, Hope; Surber, L. M. M.; Blake, Tom

doi:10.1007/s10681-009-0066-6

Cited by 15 publications

(11 citation statements)

References 61 publications

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“…This is exemplified by the QTL 'Qsch7a', which in a biparental QTL mapping study explained 47% of variation in SC [76]. In the present study, 'QTL23_SC' located in the same genomic region as 'Qsch7a' explains only 0.2% of the variation.…”

Section: Discussioncontrasting

confidence: 47%

Genome-wide association studies for agronomical traits in a world wide spring barley collection

et al. 2012

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BackgroundGenome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits. In this study we explored the genetic basis of variation for the traits heading date, plant height, thousand grain weight, starch content and crude protein content in a diverse collection of 224 spring barleys of worldwide origin. The whole panel was genotyped with a customized oligonucleotide pool assay containing 1536 SNPs using Illumina's GoldenGate technology resulting in 957 successful SNPs covering all chromosomes. The morphological trait "row type" (two-rowed spike vs. six-rowed spike) was used to confirm the high level of selectivity and sensitivity of the approach. This study describes the detection of QTL for the above mentioned agronomic traits by GWAS.ResultsPopulation structure in the panel was investigated by various methods and six subgroups that are mainly based on their spike morphology and region of origin. We explored the patterns of linkage disequilibrium (LD) among the whole panel for all seven barley chromosomes. Average LD was observed to decay below a critical level (r2-value 0.2) within a map distance of 5-10 cM. Phenotypic variation within the panel was reasonably large for all the traits. The heritabilities calculated for each trait over multi-environment experiments ranged between 0.90-0.95. Different statistical models were tested to control spurious LD caused by population structure and to calculate the P-value of marker-trait associations. Using a mixed linear model with kinship for controlling spurious LD effects, we found a total of 171 significant marker trait associations, which delineate into 107 QTL regions. Across all traits these can be grouped into 57 novel QTL and 50 QTL that are congruent with previously mapped QTL positions.ConclusionsOur results demonstrate that the described diverse barley panel can be efficiently used for GWAS of various quantitative traits, provided that population structure is appropriately taken into account. The observed significant marker trait associations provide a refined insight into the genetic architecture of important agronomic traits in barley. However, individual QTL account only for a small portion of phenotypic variation, which may be due to insufficient marker coverage and/or the elimination of rare alleles prior to analysis. The fact that the combined SNP effects fall short of explaining the complete phenotypic variance may support the hypothesis that the expression of a quantitative trait is caused by a large number of very small effects that escape detection. Notwithstanding these limitations, the integration of GWAS with biparental linkage mapping and an ever increasing body of genomic sequence information will facilitate the systematic isolation of agronomically important genes and subsequent analysis of their allelic diversity.

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Section: Discussioncontrasting

confidence: 47%

Genome-wide association studies for agronomical traits in a world wide spring barley collection

et al. 2012

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“…3) [12]. Marquez-Cedillo et al [8] and Abdel-Haleem et al [14] identified a consensus QTL near the nud locus on chromosome 7HL [8, 14]. However, the location of these QTLs was different from that detected in the present study.…”

Section: Discussioncontrasting

confidence: 79%

Identification of QTLs controlling grain protein concentration using a high-density SNP and SSR linkage map in barley (Hordeum vulgare L.)

et al. 2017

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BackgroundGrain protein concentration (GPC) is a major determinant of quality in barley (Hordeum vulgare L.). Breeding barley cultivars with high GPC has practical value for feed and food properties. The aim of the present study was to identify quantitative trait loci (QTLs) for GPC that could be detected under multiple environments.ResultsA population of 190 recombinant inbred lines (RILs) deriving from a cross between Chinese landrace ZGMLEL with high GPC (> 20%) and Australian cultivar Schooner was used for linkage and QTL analyses. The genetic linkage map spanned 2353.48 cM in length with an average locus interval of 2.33 cM. GPC was evaluated under six environments for the RIL population and the two parental lines. In total, six environmentally stable QTLs for GPC were detected on chromosomes 2H (1), 4H (1), 6H (1), and 7H (3) and the increasing alleles were derived from ZGMLEL. Notably, the three QTLs on chromosome 7H (QGpc.ZiSc-7H.1, QGpc.ZiSc-7H.2, and QGpc.ZiSc-7H.3) that linked in coupling phase were firstly identified. Moreover, the genetic effects of stable QTLs on chromosomes 2H, 6H and 7H were validated using near isogenic lines (NILs).ConclusionsCollectively, the identified QTLs expanded our knowledge about the genetic basis of GPC in barley and could be selected to develop cultivars with high grain protein concentration.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-1067-6) contains supplementary material, which is available to authorized users.

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“…High starch contents are needed in barley for brewing and feeding (Qi et al ., 2005; Abdel-Haleem et al ., 2010). The phenotype of the starch content was significantly different among the barley germplasm materials, and high-starch content varieties were present within both six-row and two-row barley.…”

Section: Discussionmentioning

confidence: 99%

“…Characterization of markers associated with economically important traits is important for subsequent breeding processes and is thus useful for the community. Previous studies based on linkage mapping (Abdel-Haleem et al ., 2010) and genome-wide association studies (GWAS) (Pasam et al ., 2012) have revealed many molecular markers associated with starch content in barley. However, it is usually expensive and time consuming to assay all individuals collected from a sample population for the target traits.…”

Section: Introductionmentioning

confidence: 99%

Identification of molecular markers for starch content in barley (Hordeum vulgare L.) by genome-wide association studies based on bulked samples

Zhang¹,

Luan²,

Zang³

et al. 2020

Plant Genet. Resour.

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Starch content is an important trait in barley. To evaluate the genetic diversity and identify molecular markers of starch content in barley, 40 cultivated barley genotypes collected from different regions, including genotypes whose starch content is at either the high or low end of the spectrum (15), were used in this study. All the genotypes were re-sequenced by the double-digest-restriction associated DNA sequencing method, and a total of 299,103 single-nucleotide polymorphism (SNP) markers were obtained. The genotypes were divided into four sub-populations based on FASTSTRUCTURE, principal component analysis and neighbour-joining tree analysis. All four sub-populations had a high linkage disequilibrium, especially group 3, whose members were recently bred for malting in the Jiangsu coastal area. The starch content of the barley lines was evaluated during three growing seasons (2014–2017), and the average values of starch content across the three growing seasons at the low and high ends were 51.5 and 55.0%, respectively. The starch content was affected by population structure, the barley in group 2 had a low starch content, while the barley in group 4 had a high starch content. Twenty-six SNP markers were identified as being significantly associated with starch content (P ⩽ 0.001) based on the average values across the three growing seasons using the mixed linear model method. These SNP markers were located on chromosomes 1H and 4H, and were considered loci of qSC1-1 and qSC4-1, respectively. The major identified QTLs for starch content are helpful for further research on carbohydrates and for barley breeding.

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Quantitative trait loci of acid detergent fiber and grain chemical composition in hulled × hull-less barley population

Cited by 15 publications

References 61 publications

Genome-wide association studies for agronomical traits in a world wide spring barley collection

Genome-wide association studies for agronomical traits in a world wide spring barley collection

Identification of QTLs controlling grain protein concentration using a high-density SNP and SSR linkage map in barley (Hordeum vulgare L.)

Identification of molecular markers for starch content in barley (Hordeum vulgare L.) by genome-wide association studies based on bulked samples

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