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Numerous quantitative trait loci (QTLs) have been identified for wheat quality; however, most are confined to low-density genetic maps. In this study, based on specific-locus amplified fragment sequencing (SLAF-seq), a high-density genetic map was constructed with 193 recombinant inbred lines derived from Chuanmai 42 and Chuanmai 39. In total, 30 QTLs with phenotypic variance explained (PVE) up to 47.99% were identified for falling number (FN), grain protein content (GPC), grain hardness (GH), and starch pasting properties across three environments. Five  NAM  genes closely adjacent to  QGPC.cib-4A  probably have effects on GPC.  QGH.cib-5D  was the only one detected for GH with high PVE of 33.31–47.99% across the three environments and was assumed to be related to the nearest  pina-D1  and  pinb-D1 genes. Three QTLs were identified for FN in at least two environments, of which  QFN.cib-3D  had relatively higher PVE of 16.58–25.74%. The positive effect of  QFN.cib-3D  for high FN was verified in a double-haploid population derived from Chuanmai 42  ×  Kechengmai 4. The combination of these QTLs has a considerable effect on increasing FN. The transcript levels of  Basic 7S globulin  and  Basic 7S globulin 2  in  QFN.cib-3D  were significantly different between low FN and high FN bulks, as observed through bulk segregant RNA-seq (BSR). These QTLs and candidate genes based on the high-density genetic map would be beneficial for further understanding of the genetic mechanism of quality traits and molecular breeding of wheat.

frontiers in plant science

Quantitative Trait Locus (QTLs) Mapping for Quality Traits of Wheat Based on High Density Genetic Map Combined With Bulked Segregant Analysis RNA-seq (BSR-Seq) Indicates That the Basic 7S Globulin Gene Is Related to Falling Number