Combined linkage analysis and association mapping identifies genomic regions associated with yield-related and drought-tolerance traits in wheat (Triticum aestivum L.)

Genetic dissection for seedling root-related traits using multiple-methods in bread wheat (Triticum aestivum L.)

KEY MESSAGE

Several quantitative trait loci (QTL) and structural chromosome variations (SCVs) related to seedling root traits were identified using multiple methods, which provided valuable insights to assist breeding efforts in wheat. The root system of wheat affects water and fertilizer use efficiency, stress tolerance, and agronomic traits. Using association analysis and linkage mapping, QTL associated with 11 seedling-stage root traits were identified with single nucleotide polymorphisms (SNPs) and SCVs under both hydroponic nutrient solution culture experiment (NCE) and vermiculite culture experiment (VCE). Except for maximum root length (MRL), the root traits of seedlings under NCE and VCE differed significantly. Root fresh weight (RFW) and root dry weight (RDW) were significantly correlated with most agronomic traits and grain yield. Identification of RFW and RDW by NCE might provide a reference basis for VCE. Co-localization analysis revealed that NCE and VCE simultaneously detected SNP-loci viz. QRdw.sxau-6A, QRd.sxau-1B.2, and QDw.sxau-6A (5.56-8.76% of R2). The SCV-loci Mr1B-3, Mr3A-3 and Mr3A-4 were detected in both NCE and VCE (4.74-9.07% of R2). Furthermore, QRdw.sxau-6A, QSfw.sxau-6A and QRd.sxau-4A were detected using the mixed linear model (MLM), 3 Variance-component multi-locus random-SNP-effect Mixed Linear Mode (3VmrMLM) and rrBLUP. In the association panel, SNPs and SCVs co-localized to 14 MTAs, of which Mr5A-6 and QRd.sxau-5A were significantly associated with root diameter (RD). The association panel and doubled haploid (DH) population co-located 10 QTL, of which QDw.sxau-1D was stably detected. Finally, QDw.sxau-6A and Mg6A-9 overlapped in same genomic location containing candidate genes TraesCS6A02G372300, TraesCS6A02G382900 and TraesCS6A02G365100. The present study contributes novel insights into the genetics of root architecture in wheat.

Linkage and association analysis to identify wheat pre-harvest sprouting resistance genetic regions and develop KASP markers

Pre-harvest sprouting (PHS) of wheat (Triticum aestivum L.) is one of the complex traits that result in rainfall-dependent reductions in grain production and quality worldwide. Breeding new varieties and germplasm with PHS resistance is of great importance to reduce this problem. However, research on markers and genes related to PHS resistance is limited, especially in marker-assisted selection (MAS) wheat breeding. To this end, we studied PHS resistance in recombinant inbred line (RIL) population and in 171 wheat germplasm accessions in different environments and genotyped using the wheat Infinium 50 K/660 K SNP array. Quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) identified 59 loci controlling PHS. Upon comparison with previously reported QTL affecting PHS, 16 were found to be new QTL, and the remaining 43 loci were co-localized with QTL from previous studies. We also pinpointed 12 candidate genes within these QTL intervals that share functional similarities with genes previously known to influence PHS resistance. In addition, we developed and validated two kompetitive allele-specific PCR (KASP) markers within the chromosome 7B region identified by linkage analysis. These QTL, candidate genes, and the KASP marker identified in this study have the potential to improve PHS resistance of wheat, and they may enhance our understanding of the genetic basis of PHS resistance, thus being useful for MAS breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01526-0.

Genome-wide association study and genomic selection of spike-related traits in bread wheat

KEY MESSAGE

Identification of 337 stable MTAs for wheat spike-related traits improved model accuracy, and favorable alleles of MTA259 and MTA64 increased grain weight and yield per plant. Wheat (Triticum aestivum L.) is one of the three primary global, staple crops. Improving spike-related traits in wheat is crucial for optimizing spike and plant morphology, ultimately leading to increased grain yield. Here, we performed a genome-wide association study using a dataset of 24,889 high-quality unique single-nucleotide polymorphisms (SNPs) and phenotypic data from 314 wheat accessions across eight diverse environments. In total, 337 stable and significant marker-trait associations (MTAs) related to spike-related traits were identified. MTA259 and MTA64 were consistently detected in seven and six environments, respectively. The presence of favorable alleles associated with MTA259 and MTA64 significantly reduced wheat spike exsertion length and spike length, while enhancing thousand kernel weight and yield per plant. Combined gene expression and network analyses identified TraesCS6D03G0692300 and TraesCS6D03G0692700 as candidate genes for MTA259 and TraesCS2D03G0111700 and TraesCS2D03G0112500 for MTA64. The identified MTAs significantly improved the prediction accuracy of each model compared with using all the SNPs, and the random forest model was optimal for genome selection. Additionally, the eight stable and major MTAs, including MTA259, MTA64, MTA66, MTA94, MTA110, MTA165, MTA180, and MTA164, were converted into cost-effective and efficient detection markers. This study provided valuable genetic resources and reliable molecular markers for wheat breeding programs.

Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

BACKGROUND

Agropyron cristatum (L.) is a valuable genetic resource for expanding the genetic diversity of common wheat. Pubing3228, a novel wheat-A. cristatum hybrid germplasm, exhibits several desirable agricultural traits, including high grain number per spike (GNS). Understanding the genetic architecture of GNS in Pubing3228 is crucial for enhancing wheat yield. This study aims to analyze the specific genetic regions and alleles associated with high GNS in Pubing3228.

METHODS

The study employed a recombination inbred line (RIL) population derived from a cross between Pubing3228 and Jing4839 to investigate the genetic regions and alleles linked to high GNS. Quantitative Trait Loci (QTL) analysis and candidate gene investigation were utilized to explore these traits.

RESULTS

A total of 40 QTLs associated with GNS were identified across 16 chromosomes, accounting for 4.25-17.17% of the total phenotypic variation. Five QTLs (QGns.wa-1D, QGns.wa-5 A, QGns.wa-7Da.1, QGns.wa-7Da.2 and QGns.wa-7Da.3) accounter for over 10% of the phenotypic variation in at least two environments. Furthermore, 94.67% of the GNS QTL with positive effects originated from Pubing3228. Candidate gene analysis of stable QTLs identified 11 candidate genes for GNS, including a senescence-associated protein gene (TraesCS7D01G148000) linked to the most significant SNP (AX-108,748,734) on chromosome 7D, potentially involved in reallocating nutrients from senescing tissues to developing seeds.

CONCLUSION

This study provides new insights into the genetic mechanisms underlying high GNS in Pubing3228, offering valuable resources for marker-assisted selection in wheat breeding to enhance yield.