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

Abstract

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-D1genes. 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.

Dissection of the Genetic Architecture for Quantities of Gliadins Fractions in Wheat (Triticum aestivum L.)

“…Previous analyses detected a series of QTLs related to the protein contents in a population derived from two parents and in a population comprising natural wheat varieties (accessions) ( Table 2 ) ( Prasad et al, 2003 ; Plessis et al, 2013 ; Nigro et al, 2019 ; Lou et al, 2021 ). The major genetic loci controlling protein contents are on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 5A, 5B, 5D, 6B, and 7B ( Cui et al, 2016 ; Nigro et al, 2019 ; Li et al, 2020 ; Lou et al, 2021 ). The QTLs associated with the gliadin content have been mapped to chromosomes 1B, 2A, 3B, 4A, 5A, 7A, and 7B ( Plessis et al, 2013 ; Zhao et al, 2017 ) ( Table 2 ).…”

High-Resolution Detection of Quantitative Trait Loci for Seven Important Yield Components in Wheat (Triticum aestivum L.) using a High-Density SALF-Seq Genetic Map

“…A whole-genome genetic map constructed previously was adopted for QTL mapping [29]. The genetic map was constructed using the CM42×CM39 RIL population with SALF markers.…”

“…The genetic map was constructed using the CM42×CM39 RIL population with SALF markers. A total of 4996 Bin SLAFs were distributed in 21 linkage groups and covered a total genetic distance of 2,859.94 cM with an average interval of 0.57 cM between adjacent Bin marker (Table S1) [29].…”

“…In the present study, a high-resolution genetic map constructed through speci c-locus amplifed fragment (SALF) sequencing was adopted for detection of yield componant QTLs in a recombinant inbred line (RIL) population derived from two elite winter wheat varieties Chuanmai42 (CM42) and Chuanmai39 (CM39) [29]. Seven traits including TGW, GW, GL, PH, GNS, SL and SNS were assessed in multiple environments to detected potential major and stable QTL, which will lay out a foundation for further study on ne mapping and cloning of the underlying key genes for yield.…”

Comparative Genomic Analysis of Quantitative Trait Loci Associated With Micronutrient Contents, Grain Quality, and Agronomic Traits in Wheat (Triticum aestivum L.)

“…Because of the large genome size and limited genome sequence information in wheat, the typical mapping intervals are quite large in most studies especially for the complex quality traits (Li Q. et al, 2020) and so further refinement is needed to narrow down the QTL intervals. Developing a statistically derived catalog of relevant loci is critical for developing marker-assisted selection (MAS) approaches in breeding programs.…”