Population-specific QTLs and their different epistatic interactions for pod dehiscence in soybean [Glycine max (L.) Merr.]

Kang, Sung-Taeg; Kwak, Myounghai; Kim, Hyeun-Kyeung; Choung, Myoung-Gun; Han, Won-Young; Baek, In-Youl; Kim, Moon Young; Van, Kyujung; Lee, Suk-Ha

doi:10.1007/s10681-008-9810-6

Cited by 49 publications

(48 citation statements)

References 28 publications

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“…In contrast to results obtained from interspecific genetic analysis, a major QTL for pod dehiscence has been identified in the cultivated species on chromosome 16 (14)(15)(16)(17). An anatomical analysis using near-isogenic lines (NILs) for this QTL, designated as qPDH1, has revealed no marked differences in suture morphology, including that of secondary cell-wall formation (18) (Fig.…”

mentioning

confidence: 76%

Molecular basis of a shattering resistance boosting global dissemination of soybean

Funatsuki

Suzuki

Hirose

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

184

223

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Pod dehiscence (shattering) is essential for the propagation of wild plant species bearing seeds in pods but is a major cause of yield loss in legume and crucifer crops. Although natural genetic variation in pod dehiscence has been, and will be, useful for plant breeding, little is known about the molecular genetic basis of shattering resistance in crops. Therefore, we performed map-based cloning to unveil a major quantitative trait locus (QTL) controlling pod dehiscence in soybean. Fine mapping and complementation testing revealed that the QTL encodes a dirigent-like protein, designated as Pdh1. The gene for the shattering-resistant genotype, pdh1, was defective, having a premature stop codon. The functional gene, Pdh1, was highly expressed in the lignin-rich inner sclerenchyma of pod walls, especially at the stage of initiation in lignin deposition. Comparisons of near-isogenic lines indicated that Pdh1 promotes pod dehiscence by increasing the torsion of dried pod walls, which serves as a driving force for pod dehiscence under low humidity. A survey of soybean germplasm revealed that pdh1 was frequently detected in landraces from semiarid regions and has been extensively used for breeding in North America, the world's leading soybean producer. These findings point to a new mechanism for pod dehiscence involving the dirigent protein family and suggest that pdh1 has played a crucial role in the global expansion of soybean cultivation. Furthermore, the orthologs of pdh1, or genes with the same role, will possibly be useful for crop improvement.

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mentioning

confidence: 76%

Molecular basis of a shattering resistance boosting global dissemination of soybean

Funatsuki

Suzuki

Hirose

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

184

223

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“…This consensus sequence spanned 915. 4 Mb, representing a coverage of 97.65% of the G. max published genome sequence and an average mapping depth of 43-fold. The nucleotide sequence of the G. soja genome, which contains 2.5 Mb of substituted bases and 406 kb of small insertions/deletions relative to G. max, is ∼0.31% different from that of G. max.…”

mentioning

confidence: 99%

Whole-genome sequencing and intensive analysis of the undomesticated soybean ( Glycine soja Sieb. and Zucc.) genome

Kim

Lee

Van

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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310

263

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The genome of soybean ( Glycine max ), a commercially important crop, has recently been sequenced and is one of six crop species to have been sequenced. Here we report the genome sequence of G. soja , the undomesticated ancestor of G. max (in particular, G. soja var. IT182932). The 48.8-Gb Illumina Genome Analyzer (Illumina-GA) short DNA reads were aligned to the G. max reference genome and a consensus was determined for G. soja . This consensus sequence spanned 915.4 Mb, representing a coverage of 97.65% of the G. max published genome sequence and an average mapping depth of 43-fold. The nucleotide sequence of the G. soja genome, which contains 2.5 Mb of substituted bases and 406 kb of small insertions/deletions relative to G. max , is ∼0.31% different from that of G. max . In addition to the mapped 915.4-Mb consensus sequence, 32.4 Mb of large deletions and 8.3 Mb of novel sequence contigs in the G. soja genome were also detected. Nucleotide variants of G. soja versus G. max confirmed by Roche Genome Sequencer FLX sequencing showed a 99.99% concordance in single-nucleotide polymorphism and a 98.82% agreement in insertion/deletion calls on Illumina-GA reads. Data presented in this study suggest that the G. soja / G. max complex may be at least 0.27 million y old, appearing before the relatively recent event of domestication (6,000∼9,000 y ago). This suggests that soybean domestication is complicated and that more in-depth study of population genetics is needed. In any case, genome comparison of domesticated and undomesticated forms of soybean can facilitate its improvement.

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“…Out of these 46 plants with 237 bp marker all but one plant had pod shattering more than 25%. Kang et al 2009), had reported that Satt166 had a minor QTL for pod dehiscence on Linkage group L. Satt166 marker was originally described by Cregan et al (1999) to be present on soybean linkage group 'L'. Kang et al, (2009) reported that Satt166 amplified marker for a minor pod dehiscence QTL that had LOD score of 3.7.…”

Section: Validation Of Markers For Pod Shattering Resistancementioning

confidence: 99%

“…Yamada et al, (2009) reported that shattering-resistant cultivars harbor recessive shattering-resistance allele at qPDH1 regardless of their origin and that molecular markers near qPDH1 could be used for markerassisted selection for shattering resistance in soybean. Kang et al (2009) reported four minor QTLs for pod dehiscence in addition to a qPDH1 which explained 46% of phenotypic variation. Suzuki et al (2010) carried out high-resolution mapping of qPDH1 to a 134-kb region on chromosome 16 (formerly linkage group J) to develop useful selection markers.…”

Section: Introductionmentioning

confidence: 99%

Molecular tagging of pod shattering tolerance trait in soybean[Glycine max (L.) Merrill] genotype MACS-450.

Thakare

Chimote

Adsul

et al. 2017

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Pod shattering (Dehiscence) severely reduces seed yield in soybean. Molecular tagging of pod shattering resistance can help in the process of breeding for shattering tolerance. In this study, an segregating population of cross (susceptible cultivar Monetta x tolerant genotype MACS-450) was used for bulked segregant analysis (BSA) with 26 SSR (simple sequence repeat) primers known to amplify markers linked to 22 qPDH loci. Among them, eight polymorphic SSR markers, viz., Sat_350 (qPDH1-7), Satt185 (qPDH1-3), Satt674 (qPDH1-5 loci), Satt166 (qPDH3-5), SRM1 (qPDH1 loci) Sat_342 (qPDH3-2), Satt685 (qPDH1-2) and Sat_407 (qPDH3-1) were able to distinguish parents differing for pod shattering of them two primers Satt 166 and SRM1 yielded markers polymorphic in between shattering tolerant and susceptible bulks by amplifying only Satt166-200 bp marker and SRM1-234bp marker only in tolerant bulks. Only Satt166-200 bp marker was observed in tolerant parent, bulks and 14 plants; while another 237 bp marker for pod shattering susceptibility got amplified in 46 plants including 8 plants that were heterozygous for both alleles. SRM1-234 bp marker was observed only in tolerant parent, bulks and 15 plants; while another 237 bp marker for pod shattering susceptibility got amplified in 45 plants. In combined marker analysis, the markers Satt 166 (qPDH3-5 loci) and SRM1 (qPDH1 loci) were linked with pod shattering score and were also confirmed in individual 60 F 2 segregants. Hence, these markers could be utilized in the marker assisted for pod shattering resistance/tolerance breeding of qPDH3-5 like and qPDH1 genes.

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Population-specific QTLs and their different epistatic interactions for pod dehiscence in soybean [Glycine max (L.) Merr.]

Cited by 49 publications

References 28 publications

Molecular basis of a shattering resistance boosting global dissemination of soybean

Molecular basis of a shattering resistance boosting global dissemination of soybean

Whole-genome sequencing and intensive analysis of the undomesticated soybean ( Glycine soja Sieb. and Zucc.) genome

Molecular tagging of pod shattering tolerance trait in soybean[Glycine max (L.) Merrill] genotype MACS-450.

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