Genetic identification and characterization of chromosomal regions for kernel length and width increase from tetraploid wheat

Abstract

Background Improvement of wheat gercTriticum aestivum L.) yield could relieve global food shortages. Kernel size, as an important component of 1000-kernel weight (TKW), is always a significant consideration to improve yield for wheat breeders. Wheat related species possesses numerous elite genes that can be introduced into wheat breeding. It is thus vital to explore, identify, and introduce new genetic resources for kernel size from wheat wild relatives to increase wheat yield. Results In the present study, quantitative trait loci (QTL) for kernel length (KL) and width (KW) were detected in a recombinant inbred line (RIL) population derived from a cross between a wild emmer accession ‘LM001’ and a Sichuan endemic tetraploid wheat ‘Ailanmai’ using the Wheat 55 K single nucleotide polymorphism (SNP) array-based constructed linkage map and phenotype from six different environments. We identified eleven QTL for KL and KW including two major ones QKL.sicau-AM-3B and QKW.sicau-AM-4B, the positive alleles of which were from LM001 and Ailanmai, respectively. They explained 17.57 to 44.28% and 13.91 to 39.01% of the phenotypic variance, respectively. For these two major QTL, Kompetitive allele-specific PCR (KASP) markers were developed and used to successfully validate their effects in three F3 populations and two natural populations containing a panel of 272 Chinese wheat landraces and that of 300 Chinese wheat cultivars, respectively. QKL.sicau-AM-3B was located at 675.6–695.4 Mb on chromosome arm 3BL. QKW.sicau-AM-4B was located at 444.2–474.0 Mb on chromosome arm 4BL. Comparison with previous studies suggested that these two major QTL were likely new loci. Further analysis indicated that the positive alleles of QKL.sicau-AM-3B and QKW.sicau-AM-4B had a great additive effect increasing TKW by 6.01%. Correlation analysis between KL and other agronomic traits showed that KL was significantly correlated to spike length, length of uppermost internode, TKW, and flag leaf length. KW was also significantly correlated with TKW. Four genes, TRIDC3BG062390, TRIDC3BG062400, TRIDC4BG037810, and TRIDC4BG037830, associated with kernel development were predicted in physical intervals harboring these two major QTL on wild emmer and Chinese Spring reference genomes. Conclusions Two stable and major QTL for KL and KW across six environments were detected and verified in three biparental populations and two natural populations. Significant relationships between kernel size and yield-related traits were identified. KASP markers tightly linked the two major QTL could contribute greatly to subsequent fine mapping. These results suggested the application potential of wheat related species in wheat genetic improvement.

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

“…For example, QTL conferring SNS, SL, KNS, and TKW were co-located at Xgwm126 – Xgwm291 (672.92–700.49 Mb; Wang et al, 2011 ); QHd.sau-5A , QAn.sau-5A , QPht.sau-5A , QSl.sau-5A1 , and QSd.sau-5A1 were co-located at wPt-9094–wPt-9513 (435.00–536.98 Mb; Luo et al, 2016 ). Compared with kernel size-related QTL in the AM population, no QTL for such as KL and KW were detected on chromosome 5A ( Zhou et al, 2021 ). Additionally, QSd.sau-AM-5A.2 (624.11–626.14 Mb on wild emmer genome) in the present study and QSns.sau-AM-5A (557.72–571.41 Mb; Mo et al, 2021 ) are not co-located in the same region.…”

“…The phenotype values for SNS in 2018KB were determined by Ding et al (2021) , and the SNS data across remainder environments was determined by Liu et al (2020) . The agronomic traits of the AM population were measured by Mo et al (2021) (PH, AD, TKW, SL, SNS, PTN, KNL and KNS) and Zhou et al (2021) (KL, KW). The phenotypic data of SL and SNS in the 2CM population were measured by Ma et al (2019a) .…”

Mapping and validation of major and stable QTL for flag leaf size from tetraploid wheat

“…An RIL and two F 3 populations with Ailanmai (AL) as a common parent were used in this study. They were AL/LM001 (AM, 121 F 8 RILs) (Mo et al., 2021), AL/PI 503554 (AP, 54 F 3 lines), and AL/PI 193877 (API, 70 F 3 lines) (Zhou et al., 2021). Ailanma ( T. turgidum L., 2 n = 28, AABB) is a dwarf Chinese landrace with wide flag leaf.…”

“…Both FLA and FLR are derivative characteristics and based on the following equations: FLA = FLW × FLL × 0.75 (Edae et al., 2013; Zeuli & Qualset., 2010) and FLR = FLL/FLW. The datasets of FLL and FLW (except 2021CZ and 2021WJ) were used for correlation analysis in our previous study (Zhou et al., 2021) (Supplemental Table S1). We also measured the phenotypic values of yield‐related traits.…”

QTL cluster analysis and marker development for kernel traits based on DArT markers in spring bread wheat (Triticum aestivum L.)

“…In recent years, with the release of the wheat and closely related species genome sequence, and numerous transcriptome datasets (Duan et al, 2012;Kumar et al, 2015;Yang et al, 2022), all of these might lead to greater convenience for gene mapping, discovery of candidate genes, gene cloning, and development of markers, especially in the area of marker development, such as simple sequence repeat (SSR) markers, cleaved amplified polymorphic sequence (CAPS) markers, kompetitive allelespecific PCR (KASP) markers, and semi-thermal asymmetric reverse PCR (STARP) markers (Wu et al, 2020). The rapid evolution of molecular technology has provided powerful tools to dissect complex traits ; many molecular markers for kernel traits have been developed, especially in KASP markers, for example, KASP-AX-111112626 (tightly linked to kernel length QTL QKL.sicau-AM-3B), KASP-AX-108974756 (tightly linked to kernel width QTL QKW.sicau-AM-4B) (Zhou et al, 2021), and KASP-AX-109379070 (tightly linked to kernel length QTL QKL.sicau-2SY-1B) (Qu et al, 2021). The development of these markers has accelerated the rapid development of wheat molecular breeding.…”