Mapping QTL for agronomic traits in breeding populations

Würschum, Tobias

doi:10.1007/s00122-012-1887-6

Cited by 200 publications

(142 citation statements)

References 69 publications

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“…So far, QTL studies for MRDD resistance in maize have been mainly based on linkage mapping; most QTLs are population-specific, and the genetic variation detected in a specific bi-parental population may not be transferable to other populations. By contrast, QTLs identified in elite breeding germplasms are of direct relevance for crop improvement via knowledge-based breeding, and can be immediately used for MAS approaches (Würschum 2012;Wang et al 2012). In the present study, a set of 184 elite maize inbred lines from modern breeding programs was evaluated to identify QTLs associated with MRDD resistance in different years through genome-wide association analysis, with the aim of resistance-pyramiding to improve breeding efficiency by MAS.…”

Section: Introductionmentioning

confidence: 97%

Identification of significant single nucleotide polymorphisms for resistance to maize rough dwarf disease in elite maize (Zea mays L.) inbred lines

Hao¹,

Cheng²,

Chen³

et al. 2014

Euphytica

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Maize rough dwarf disease (MRDD) is a devastating viral disease that causes considerable yield losses in maize worldwide. Identifying quantitative trait loci underlying resistance to MRDD is important for genetic improvement of maize. In this study, 184 elite maize inbred lines from modern breeding programs were evaluated in three years to identify QTLs for MRDD resistance using 3072 single-nucleotide polymorphisms (SNPs) via genome-wide association analysis. The analysis revealed abundant phenotypic diversity in the studied population. All tested maize inbred lines were divided into two subpopulations based on a Bayesian model, and the linkage disequilibrium (LD) level differed among chromosomes, with an intra-chromosomal average of 1,000-1,500 kb. After correction for multiple testing, 21 SNPs were identified for MRDD resistance in different years as well as for BLUPs (the best linear unbiased predictions) of MRDD resistance based on the MLM model, one SNP of PZE-101245575 was stably possessed the most promising association. Several SNPs were located in or close to previously reported quantitative trait loci for MRDD resistance. The significant SNPs identified in this study will be helpful for further understanding the genetic basis of MRDD resistance, and might facilitate the pyramiding of favorable alleles for high resistance to MRDD in future marker-assisted selection schemes in maize.

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Section: Introductionmentioning

confidence: 97%

Identification of significant single nucleotide polymorphisms for resistance to maize rough dwarf disease in elite maize (Zea mays L.) inbred lines

Hao¹,

Cheng²,

Chen³

et al. 2014

Euphytica

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“…Association mapping has been developed by human geneticists but in recent years has been adopted by plant geneticists and become an increasingly popular genomic tool to dissect the genetic architecture of complex traits in plants (Nordborg and Weigel, 2008;Hamblin et al, 2011;Würschum, 2012). It has successfully been used to detect quantitative trait loci (QTL) for agronomically important traits in many crop species including maize (for example, Harjes et al, 2008), wheat (for example, Breseghello and Sorrells, 2006;Reif et al, 2011a, b), barley (for example, Wang et al, 2012;Berger et al, 2013) and rice (for example, Huang et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of multi-locus models for genome-wide association studies: a case study in sugar beet

Würschum

Kraft²

2014

Heredity

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Association mapping has become a widely applied genomic approach to dissect the genetic architecture of complex traits. A major issue for association mapping is the need to control for the confounding effects of population structure, which is commonly done by mixed models incorporating kinship information. In this case study, we employed experimental data from a large sugar beet population to evaluate multi-locus models for association mapping. As in linkage mapping, markers are selected as cofactors to control for population structure and genetic background variation. We compared different biometric models with regard to important quantitative trait locus (QTL) mapping parameters like the false-positive rate, the QTL detection power and the predictive power for the proportion of explained genotypic variance. Employing different approaches we show that the multilocus model, that is, incorporating cofactors, outperforms the other models, including the mixed model used as a reference model. Thus, multi-locus models are an attractive alternative for association mapping to efficiently detect QTL for knowledgebased breeding.

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“…To sum up, despite some discrepancies, many of the loci that were identified in this study were associated with traits common with previous studies indicating the creditability of the results, though relatively small number of markers used. Also, though the percentages of the variance explained by the associated markers are seemingly low ranging from 2.6 to 17.76% (Table 1), these estimates are lower than the real QTL effects because in association mapping approach incomplete LD between marker and QTL leads to an underestimation of the variance explained by the QTL (Wurschum, 2012). Comparable results between biparental mapping population QTL analysis and association mapping could be observed when LD is perfect (r 2 =1) and the same alleles segregate in both populations (Myles et al, 2009).…”

Section: Thousand Grain Weightmentioning

confidence: 94%

Evaluation and association mapping of agronomic traits for drought tolerance in sorghum [Sorghum bicolor (L.) Moench]

Endre¹,

Bantte²

2017

Afr. J. Biotechnol.

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Drought is the major sorghum production constraint in Ethopia which necessitates the identification of sorghum genotypes that carry genes (quantitative trait locus, QTL) associated with drought tolerance thereby developing drought tolerant sorghum varieties. The objectives of this study were to identify drought tolerant sorghum genotypes, map chromosomal regions (QTLs) associated with agronomically important traits and identify simple sequence repeat (SSR) markers tightly linked with these QTLs. One hundred and sixty (160) sorghum genotypes (152 landraces and 8 released varieties) were genotyped with 39 SSRs markers and evaluated in the field at Kobo in the off-season using an alpha lattice design replicated three times. Phenotypic data including days to 50% flowering, plant height, panicle weight, grain weight, grain weight per panicle, panicle harvest index, one thousand grain weight and number of grains per panicle were collected. Analysis of variance showed highly significant (P<0.0001) differences among the genotypes for all characters. Most of the characters showed moderate to high phenotypic and genotypic coefficient of variation. Linkage disequilibrium (LD) analysis indicated that in all accessions, 107 loci pairs (32.92%) had a significant (p< 0.05) mean LD of 0.19, with R 2 > 0.2 for 33 evaluated loci pairs. Population structure analysis showed that there were four distinct clusters in the studied materials. A total of 10 marker-trait associations were identified using seven different SSR markers. The percentage of the total variation explained by the markers ranged from 2.6% (Xtxp114 with THGT) to 17.76% (Xtxp145 with PHT). The seven SSR markers (xcup53, bSbCIR223, Xtxp114, mSbCIR248, Xtxp145, Xtxp278, and gbsp123) were located on chromosomes 1, 2, 3, 5, 6, 7 and 8, respectively, each chromosome harboring one marker. Most of the identified markers were localized in chromosomal positions that have been previously reported as positions for drought tolerance-related traits, supporting the present findings. The results of this study can serve as initial effort for the association mapping studies in sorghum particularly in Ethiopia as the associated SSR markers are potential candidates for marker-assisted selection to improve drought tolerance in sorghum. However, as this study is the first attempt in the identification of QTLs for drought tolerance using association mapping, the identified QTLs need to be validated in independent or related populations and in different environments before their use in marker-assisted selection.

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Mapping QTL for agronomic traits in breeding populations

Cited by 200 publications

References 69 publications

Identification of significant single nucleotide polymorphisms for resistance to maize rough dwarf disease in elite maize (Zea mays L.) inbred lines

Identification of significant single nucleotide polymorphisms for resistance to maize rough dwarf disease in elite maize (Zea mays L.) inbred lines

Evaluation of multi-locus models for genome-wide association studies: a case study in sugar beet

Evaluation and association mapping of agronomic traits for drought tolerance in sorghum [Sorghum bicolor (L.) Moench]

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