QTL Location and Epistatic Effect Analysis of 100-Seed Weight Using Wild Soybean (Glycine soja Sieb. & Zucc.) Chromosome Segment Substitution Lines

Increasing the yield of soybean (Glycine max L. Merrill) is a main aim of soybean breeding. The 100-seed weight is a critical factor for soybean yield. To facilitate genetic analysis of quantitative traits and to improve the accuracy of marker-assisted breeding in soybean, a valuable mapping population consisting of 194 chromosome segment substitution lines (CSSLs) was developed. In these lines, different chromosomal segments of the Chinese cultivar Suinong 14 were substituted into the genetic background of wild soybean (Glycine soja Sieb. & Zucc.) ZYD00006. Based on these CSSLs, a genetic map covering the full genome was generated using 121 simple sequence repeat (SSR) markers. In the quantitative trait loci (QTL) analysis, twelve main effect QTLs (qSW-B1-1/2/3, qSW-D1b-1/2, qSW-D2-1/2, qSW-G-1/2/3, qSW-M-2 and qSW-N-2) underlying 100-seed weight were identified in 2011 and 2012. The epistatic effects of pairwise interactions between markers were analyzed in 2011 and 2012. The results clearly demonstrated that these CSSLs could be used to identify QTLs, and that an epistatic analysis was able to detect several sites with important epistatic effects on 100-seed weight. Thus, we identified loci that will be valuable for improving soybean 100-seed weight. These results provide a valuable foundation for identifying the precise location of genes of interest, and for designing cloning and marker-assisted selection breeding strategies targeting the 100-seed weight of soybean.

• Publication year

  2016

• Venue

  PLoS ONE

• Publication date

  2016-03-02

• Fields of study

  Agricultural and Food Sciences, Medicine, Biology

• Identifiers
  DOI 10.1371/journal.pone.0149380PMID 26934088PMCID 4774989
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• Pairwise marker interaction analysis detected several loci with important epistatic effects on 100-seed weight.

  Confidence 0.93

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• Twelve main-effect QTLs for 100-seed weight were identified across the 2011 and 2012 evaluations.

  Confidence 0.95

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• A genome-wide genetic map was constructed from the CSSLs using 121 simple sequence repeat markers.

  Confidence 0.96

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• A set of 194 chromosome segment substitution lines was developed with Suinong 14 introgressions in the wild soybean background ZYD00006.

  Confidence 0.98

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review

• 100-seed weight

  trait

  The soybean yield-related trait measured as the weight of 100 seeds.

  Aliases: seed weight

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• chromosome segment substitution lines

  mapping population

  A soybean mapping population carrying donor chromosome segments introgressed into a recurrent genetic background.

  Aliases: CSSLs

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• epistatic effects

  genetic interaction

  Non-additive interactions between pairs of genetic markers evaluated for their influence on the trait.

  Aliases: epistasis

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• genetic map

  genetic map

  A genome-wide linkage map assembled from the marker data in the substitution-line population.

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• main-effect qtls

  quantitative trait loci

  Quantitative trait loci analyzed for their individual effects on the 100-seed weight trait.

  Aliases: QTLs

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• simple sequence repeat markers

  marker set

  Microsatellite DNA markers used to genotype the substitution lines and build the map.

  Aliases: SSR markers, SSRs

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• suinong 14

  cultivar, donor parent

  The Chinese soybean cultivar used as the donor source of substituted chromosomal segments.

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review
• zyd00006

  wild soybean accession, recipient parent

  The wild soybean accession that provided the recipient genetic background for the substitution lines.

  Aliases: wild soybean ZYD00006

  박진우 (dztg5apj7m) extractionAK (4715169a40) reviewKiller Whale (322360f1c1) reviewB (s683577b42) review

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