Identification of a major and stable QTL on chromosome 5A confers spike length in wheat (Triticum aestivum L.)

Abstract

Spike length (SL) is the key determinant of plant architecture and yield potential. In this study, 193 recombinant inbred lines (RILs) derived from a cross between 13F10 and Chuanmai 42 (CM42) were evaluated for spike length in six environments. Sixty RILs consisting of 30 high and 30 low SLs were genotyped using the bulked segregant analysis exome sequencing (BSE-Seq) analysis for preliminary quantitative trait locus (QTL) mapping. A 6.69 12 Mb) region on chromosome 5AL was found to have a signi cant effect on the SL trait. Fifteen kompetitive allele speci c PCR (KASP) markers were successfully converted from the single nucleotide polymorphisms (SNPs) in the SL target region. Combined with four novel simple sequence repeat (SSR) markers, a genetic linkage map spanning 21.159 cM was constructed. The mapping result con rmed the identity of a major and stable QTL named QSl.cib-5A in the targeted region that explained 7.88-26.60% of the phenotypic variation in SL. QSl.cib-5A was narrowed to a region of 4.84 cM interval corresponding to a 4.67 Mb (516.60-521.27 Mb) physical region in the Chinese Spring RefSeq v2.0 containing 17 high-con dence genes with 25 transcripts. In addition, this QTL exhibited pleiotropic effects on spikelet density (SD), with the phenotypic variances proportion ranging from 11.34-19.92%. This study provides a foundational step for cloning the QSl.cib-5A, which is involved in the regulation of spike morphology in common wheat.

Genome-wide association study of yield-related traits in common wheat (Triticum aestivum L.) under normal and drought treatment conditions

“…Under the drought treatment conditions, TGW, GW, and SL were reduced by 4, 2, and 6% compared to the normal conditions ( Figure 1 and Table 1 ). However, the broad sense heritability of TGW, GL, GW, and SL was relatively high (76.16 – 95.66%) under both conditions, consistent with previous studies ( Sukumaran et al., 2018 ; Wolde et al., 2019 ; Ji et al., 2021 ; Wang et al., 2021 ; Wang et al., 2022 ). Furthermore, the association panel showed significant phenotypic variation in TGW, GL, GW, and SL under normal and drought conditions.…”

Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations

“…To identify whether QSd.sau-AM-5A.2 is co-located with QTL or genes for SNS or SL reported previously, based on the comparison of QTL for SNS on chromosome 5A with previous studies ( Mo et al, 2021 ), we reviewed the recently published articles related to SL and SNS ( Supplementary Table 8 ). Results showed that many SL or SNS related loci located on chromosome 5AL, but most of the reported QTL or genes were at least tens of Mb away from QSd.sau-AM-5A.2 detected in this study, such as QSl.cib-5A (516.60–521.27 Mb; Ji et al, 2021 ), QTgw.cau.5A_140-142 (698.00–705.40 Mb) and QSsi.cau.5A_91 (586.61–589.22 Mb; Wang et al, 2021 ), QSl.wa-5AL.e1 / QSl.wa-5AL.e2 / QSns. wa-5AL.e1 / QSns.wa-5AL.e2 / QSns.wa-5AL.e3 / QGns.wa-5AL.e2 / QTgw.wa-5AL.e2 / QTgw.wa-5AL.e3 (672.92–700.49 Mb; Wang et al, 2011 ).…”

Fine mapping of the Hairy glume (Hg) gene in a chromosome variation region at the distal terminus of 1AS

“…Allelic frequency with the significance of linearity was performed using Euclidean distance (ED; Hill et al, 2013 ). ED value of each locus was calculated, the 4 th power of the original ED was set as correlation value to eliminate background noise, and Loess was used to fit the ED value ( Ji et al, 2021 ). varBScore was also used for BSE-Seq analysis ( Dong et al, 2020 ).…”