Fine mapping of the genetic locus <i>L1</i> conferring black pods using a chromosome segment substitution line population of soybean

He, Qingyuan; Yang, Huanming; Xiang, Shihua; Tian, Dagang; Wang, Wubin; Zhao, Tuanjie; Gai, Junyi

doi:10.1111/pbr.12272

Cited by 25 publications

(22 citation statements)

References 48 publications

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“…3o). He et al (2015) inferred that of the 13 gene candidates located in their fine‐mapped Chr 19 L2–l2 region, Glyma19g27460 was the most likely candidate; however, that candidate gene has a bp position located ∼2.75 Mbp downstream from our region of 48 significant SNPs (i.e., 36,397,778–38,521,183 on Chr 19). The reason for this substantive localization difference between our study and their study is not clear.…”

Section: Resultsmentioning

confidence: 92%

“…¶ This column lists the detected classical loci (cloned or not). The L1‐l1 locus has not yet been cloned, but was recently fine‐mapped by He et al (2015) to a Chr 19 region of 13 potential candidate genes. Of those 13, the Glyma gene listed in this table for L1–l1 was inferred by He et al (2015) as the causal gene but that inference has not yet been experimentally verified.…”

Section: Resultsmentioning

confidence: 99%

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Genome‐wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection

et al. 2017

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Genome-wide association (GWA) has been used as a tool for dissecting the genetic architecture of quantitatively inherited traits. We demonstrate here that GWA can also be highly useful for detecting many major genes governing categorically defined phenotype variants that exist for qualitatively inherited traits in a germplasm collection. Genome-wide association mapping was applied to categorical phenotypic data available for 10 descriptive traits in a collection of ∼13,000 soybean [ (L.) Merr.] accessions that had been genotyped with a 50,000 single nucleotide polymorphism (SNP) chip. A GWA on a panel of accessions of this magnitude can offer substantial statistical power and mapping resolution, and we found that GWA mapping resulted in the identification of strong SNP signals for 24 classical genes as well as several heretofore unknown genes controlling the phenotypic variants in those traits. Because some of these genes had been cloned, we were able to show that the narrow GWA mapping SNP signal regions that we detected for the phenotypic variants had chromosomal bp spans that, with just one exception, overlapped the bp region of the cloned genes, despite local variation in SNP number and nonuniform SNP distribution in the chip set.

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Section: Resultsmentioning

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Genome‐wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection

et al. 2017

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“…The pod colors of soybeans include black, brown and tan types, and are controlled by two classical genetic loci, L1 and L2 (Woodworth & Veatch, ; Bernard, ; Kiang, ). The potential causal gene of the L1 locus, Glyma19g27460 ( Wm82.a1.v1 )/Glyma.19G101700 ( Wm82.a2.v1 ), has recently been identified by fine mapping (He et al ., ). Glyma19g27460/Glyma.19G101700 encodes a MYB transcription factor and is expressed at high levels in black pods.…”

Section: Genes Underlying Domestication‐related Traitsmentioning

confidence: 97%

Soybean domestication: the origin, genetic architecture and molecular bases

2017

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SummaryDomestication provides an important model for the study of evolution, and information learned from domestication research aids in the continued improvement of crop species. Recent progress in de novo assembly and whole-genome resequencing of wild and cultivated soybean genomes, in addition to new archeological discoveries, sheds light on the origin of this important crop and provides a clearer view on the modes of artificial selection that drove soybean domestication and diversification. This novel genomic information enables the search for polymorphisms that underlie variation in agronomic traits and highlights genes that exhibit a signature of selection, leading to the identification of a number of candidate genes that may have played important roles in soybean domestication, diversification and improvement. These discoveries provide a novel point of comparison on the evolutionary bases of important agronomic traits among different crop species.

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“…CSSLs have the potential to enrich the diversity of genetic background and uncover favorable alleles related to important fiber yield and quality traits (Ali et al 2010;Wu et al 2010;Tyagi et al 2014). In addition, CSSLs are ideal materials for QTL mapping, genetic effects identifying and gene cloning (Yang et al 2015), and are more convenient to study the minor and dominant effects of genes (Wan et al 2004;He et al 2015;Li et al 2016;Qiao et al 2016). In this study, the female parent MBI7561 was selected from a CSSL constructed by G.h and G.b, which had stable and significant advantages for fiber quality compared with the recurrent parent of CCRI45, to produce BC 5 F 1 (Table 4).…”

Section: Selection Of Genetic Linkage Map and Importance Of Csslsmentioning

confidence: 99%

QTL mapping and genetic effect of chromosome segment substitution lines with excellent fiber quality from Gossypium hirsutum × Gossypium barbadense

Liú

Kong

et al. 2019

Mol Genet Genomics

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Chromosome segment substitution lines (CSSLs) are ideal materials for identifying genetic effects. In this study, CSSL MBI7561 with excellent fiber quality that was selected from BC 4 F 3:5 of CCRI45 (Gossypium hirsutum) × Hai1 (Gossypium barbadense) was used to construct 3 secondary segregating populations with 2 generations (BC 5 F 2 and BC 5 F 2:3). Eighty-one polymorphic markers related to 33 chromosome introgressive segments on 18 chromosomes were finally screened using 2292 SSR markers which covered the whole tetraploid cotton genome. A total of 129 quantitative trait loci (QTL) associated with fiber quality (103) and yield-related traits (26) were detected on 17 chromosomes, explaining 0.85-30.35% of the phenotypic variation; 39 were stable (30.2%), 53 were common (41.1%), 76 were new (58.9%), and 86 had favorable effects on the related traits. More QTL were distributed in the Dt subgenome than in the At subgenome. Twenty-five stable QTL clusters (with stable or common QTL) were detected on 22 chromosome introgressed segments. Finally, the 6 important chromosome introgressed segments (Seg-A02-1, Seg-A06-1, Seg-A07-2, Seg-A07-3, Seg-D07-3, and Seg-D06-2) were identified as candidate chromosome regions for fiber quality, which should be given more attention in future QTL fine mapping, gene cloning, and marker-assisted selection (MAS) breeding.

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Fine mapping of the genetic locus L1 conferring black pods using a chromosome segment substitution line population of soybean

Cited by 25 publications

References 48 publications

Genome‐wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection

Genome‐wide Association Mapping of Qualitatively Inherited Traits in a Germplasm Collection

Soybean domestication: the origin, genetic architecture and molecular bases

QTL mapping and genetic effect of chromosome segment substitution lines with excellent fiber quality from Gossypium hirsutum × Gossypium barbadense

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