Identification and Validation of a Novel Locus Controlling Spikelet Number in Bread Wheat (Triticum aestivum L.)

Abstract

Spikelet number is an important target trait for wheat yield improvement. Thus, the identification and verification of novel quantitative trait locus (QTL)/genes controlling spikelet number are essential for dissecting the underlying molecular mechanisms and hence for improving grain yield. In the present study, we constructed a high-density genetic map for the Kechengmai1/Chuanmai42 doubled haploid (DH) population using 13,068 single-nucleotide polymorphism (SNP) markers from the Wheat 55K SNP array. A comparison between the genetic and physical maps indicated high consistence of the marker orders. Based on this genetic map, a total of 27 QTLs associated with total spikelet number per spike (TSN) and fertile spikelet number per spike (FSN) were detected on chromosomes 1B, 1D, 2B, 2D, 3D, 4A, 4D, 5A, 5B, 5D, 6A, 6B, and 7D in five environments. Among them, five QTLs on chromosome 2D, 3D, 5A, and 7D were detected in multiple environments and combined QTL analysis, explaining the phenotypic variance ranging from 3.64% to 23.28%. Particularly, QTsn/Fsn.cib-3D for TSN and FSN [phenotypic variation explained (PVE) = 5.97–23.28%, limit of detection (LOD) = 3.73–18.51] is probably a novel locus and located in a 4.5-cM interval on chromosome arm 3DL flanking by the markers AX-110914105 and AX-109429351. This QTL was further validated in other two populations with different genetic backgrounds using the closely linked Kompetitive Allele-Specific PCR (KASP) marker KASP_AX-110914105. The results indicated that QTsn/Fsn.cib-3D significantly increased the TSN (5.56–7.96%) and FSN (5.13–9.35%), which were significantly correlated with grain number per spike (GNS). We also preliminary analyzed the candidate genes within this locus by sequence similarity, spatial expression patterns, and collinearity analysis. These results provide solid foundation for future fine mapping and cloning of QTsn/Fsn.cib-3D. The developed and validated KASP markers could be utilized in molecular breeding aiming to increase the grain yield in wheat.

High-resolution detection of quantitative trait loci for seven important yield-related traits in wheat (Triticum aestivum L.) using a high-density SLAF-seq genetic map

“…Wheat yield is a complex quantitative trait controlled by multiple genes and significantly influenced by interacting genetic and environmental factors [ 3 , 4 ]. By contrast, yield components including thousand grain weight (TGW), grain number per spike (GNS), grain width (GW), grain length (GL), plant height (PH), spike length (SL) and spikelet number per spike (SNS) typically show higher heritability than that of the yield [ 5 – 7 ].…”

“…Quantitative trait loci (QTL) mapping provides an effective approach to dissect the genetic architecture of complex quantitative traits. Over the past decades, numerous QTLs associated with yield or yield-related traits have been identified on all wheat chromosomes [ 3 , 4 , 11 , 24 – 30 ]. For example, Rht8 located on chromosome 2DS was closely linked with marker xfdc53 and reduced plant height by 10% [ 31 ]; Rht25 on wheat chromosome arm 6AS showed pleiotropic effects on coleoptile length, heading date, SL, SNS and grain weight [ 32 ].…”

“…With the development of high-throughput sequencing technology, Single nucleotide polymorphisms (SNP) markers have been widely applied to construct high-density genetic maps for QTL mapping, due to their extensive and intensive distribution throughout genomes in many crop s[ 3 , 36 – 38 ]. Specific-locus amplified fragment sequencing (SLAF-seq) was developed for economic and efficient high-throughput SNP discovery through restriction-site associated DNA tag sequencing (RAD-seq), which can provide abundant InDel and SNP markers to construct high-density genetic map [ 39 – 41 ].…”

The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat (Triticum turgidum L.) Population: Chinese Landrace “Ailanmai” × Wild Emmer

“…It is a complex quantitative trait greatly affected by genetic and environmental factors (Gao et al, 2019 ; Kuzay et al, 2019 ). Therefore, dissecting the genetic mechanism of SNS at the quantitative trait locus (QTL) level can provide more insights into the role of SNS in yield formation (Ma et al, 2019a ; Yao et al, 2019 ; Chen et al, 2020 ; Li et al, 2021 ).…”

The 55K SNP-Based Exploration of QTL for Spikelet Number Per Spike in a Tetraploid Wheat (Triticum turgidumL.) Population: Chinese Landrace ‘Ailanmai’ × Wild Emmer

“…It is a complex quantitative trait greatly affected by genetic and environmental factors (Gao et al, 2019; Kuzay et al, 2019). Therefore, dissecting the genetic mechanism of SNS at the QTL level can provide more insights into the role of SNS in yield formation (Ma et al, 2019a; Yao et al, 2019; Chen et al, 2020; Li et al, 2021).…”