Multiple-line cross quantitative trait locus mapping in sugar beet (Beta vulgaris L.)

Schwegler, Diana D.; Liu, Wenxin; Gowda, Manje; Würschum, Tobias; Schulz, Britta; Reif, Jochen C.

doi:10.1007/s11032-012-9788-6

Cited by 6 publications

(7 citation statements)

References 34 publications

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“…In comparison to single bi-parental family analyses, the use of joint analyses has proved to optimize QTL detection in carrot (Le Clerc et al 2015), maize (Blanc et al 2006; Steinhoff et al 2011), oil palm (Billotte et al 2010), perennial ryegrass (Pauly et al 2012), and sugar beet (Schwegler et al 2013). While a single bi-parental family takes into account only two alleles from each parent and allelic effects are specific to the family, connected multi-parental families can provide estimates for the allelic effects of different parental lines.…”

Section: Discussionmentioning

confidence: 99%

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

et al. 2016

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Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental families are typically unreplicated, the genetic backgrounds may contain similar progenitors previously selected due to their contribution of favorable alleles. In this study, we investigated the utility of joint QTL identification provided by analyzing half-sib families. The genetic control of powdery mildew was studied using two half-sib F1 families, namely GE0711/1009 (MN1264 × MN1214; N = 147) and GE1025 (MN1264 × MN1246; N = 125) with multiple species in their ancestry. Maternal genetic maps consisting of 1077 and 1641 single nucleotide polymorphism (SNP) markers, respectively, were constructed using a pseudo-testcross strategy. Ratings of field resistance to powdery mildew were obtained based on whole-plant evaluation of disease severity. This 2-year analysis uncovered two QTLs that were validated on a consensus map in these half-sib families with improved precision relative to the parental maps. Examination of haplotype combinations based on the two QTL regions identified strong association of haplotypes inherited from ‘Seyval blanc’, through MN1264, with powdery mildew resistance. This investigation also encompassed the use of microsatellite markers to establish a correlation between 206-bp (UDV-015b) and 357-bp (VViv67) fragment sizes with resistance-carrying haplotypes. Our work is one of the first reports in grapevine demonstrating the use of SNP-based maps and haplotypes for QTL identification and tagging of powdery mildew resistance in half-sib families.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-016-0586-4) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

et al. 2016

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“…The QTLs detected in all individual environments were named common QTLs while those detected only in subsets of environments were denoted as environment‐specific QTLs. We defined QTLs as coincident when the peaks where within a range of 20 cM of genetic map distance, following the suggestion by Schwegler et al (2013).…”

Section: Methodsmentioning

confidence: 99%

Identification of Quantitative Trait Loci Underlying Plant Height and Seed Weight in Soybean

Liu

Reif

et al. 2013

The Plant Genome

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For clarifying the genetic base of the variation of yieldrelated traits in soybean [Glycine max (L.) Merr.], we mapped quantitative trait loci (QTLs) for plant height and seed weight using a recombinant inbred line population derived from a cross between Chinese elite line Zhongpin03-5373 and cultivar Zhonghuang13. We detected 11 QTLs for plant height and 18 QTLs for seed weight across six diverse environments. These included three pairs of plant height-vs. seed weight-related QTLs located in close proximity to each other, with two pairs, qPH-7 vs. qSW-7-2 and qPH-19-2 vs. qSW-19, sharing the same direction of additive effects. Individual QTLs explained 2.02 to 47.60% of the variation in plant height and 2.13 to 14.35% in seed weight. Two and five of the major QTLs discovered for plant height and seed weight, respectively, that were stable across environments in our study have been reported previously. Among them, four QTLs,, and qSW-18, were not involved in digenic epistatic interaction in our biparental population, indicating that these QTLs will be useful for marker-assisted selection and should be targeted for the future identification of candidate genes. Moreover, eight QTLs for both plant height and seed weight were newly identified in our population.

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“…The walk speed was set to 1 cM, and the probability for markers entering the model via stepwise regression was set to 0.001. A LOD threshold of 2.5 was applied to call a QTL, and a pair of neighboring QTL was deemed to be coincident when they mapped within 20 cM of one another (Schwegler et al, 2013). Quantitative trait loci designations were based on the McCouch et al (1997) system.…”

Section: Linkage Mapping and Quantitative Trait Loci Detectionmentioning

confidence: 99%

Dissecting the Genetic Basis of Resistance to Soybean Cyst Nematode Combining Linkage and Association Mapping

Xuehui

et al. 2016

The Plant Genome

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A set of 585 informative single-nucleotide polymorphism (SNP) loci was used to genotype both a panel of diverse accessions and a set of recombinant inbred lines (RILs) bred from the cross Zhongpin03-5373 (ZP; resistant to SCN)  Zhonghuang13 (ZH; susceptible). The SNP loci are mostly sited within genic sequence in regions of the soybean [Glycine max (L.) Merr.] genome thought to harbor genes determining resistance to the soybean cyst nematode (SCN, Heterodera glycines Ichinohe). The three strongest quantitative trait nucleotides (QTNs) identified by association mapping (AM) involved the genes Glyma18 g02590 (a component of the multigene locus rhg1-b), Glyma11 g35820 and Glyma11 g35810 (an rhg1-b paralog), as well as some other loci with smaller effects. The linkage mapping (LM) analysis performed using the RILs revealed two putative quantitative trait loci (QTL): one mapping to rhg1-b and the other to an rhg1-b paralog; both of these loci were also identified by AM. The former locus explained 25.5% of the phenotypic variance for SCN resistance and the latter 5.8%. In combination, the two major loci acted nonadditively, providing a high level of SCN resistance.

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Multiple-line cross quantitative trait locus mapping in sugar beet (Beta vulgaris L.)

Cited by 6 publications

References 34 publications

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps

Identification of Quantitative Trait Loci Underlying Plant Height and Seed Weight in Soybean

Dissecting the Genetic Basis of Resistance to Soybean Cyst Nematode Combining Linkage and Association Mapping

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