Unlocking the relationships among population structure, plant architecture, growing season, and environmental adaptation in Henan wheat cultivars.

BACKGROUND: Ecological environments shape plant architecture and alter the growing season, which provides the basis for wheat genetic improvement. Therefore, understanding the genetic basis of grain yield and yield-related traits in specific ecological environments is important. RESULTS: A structured panel of 96 elite wheat cultivars grown in the High-yield zone of Henan province in China was genotyped using an Illumina iSelect 90 K SNP assay. Selection pressure derived from ecological environments of mountain front and plain region provided the initial impetus for population divergence. This determined the dominant traits in two subpopulations (spike number and spike percentage were dominance in subpopulation 2:1; thousand-kernel weight, grain filling rate (GFR), maturity date (MD), and fertility period (FP) were dominance in subpopulation 2:2), which was also consistent with their inheritance from the donor parents. Genome wide association studies identified 107 significant SNPs for 12 yield-related traits and 10 regions were pleiotropic to multiple traits. Especially, GY was co-located with MD/FP, GFR and HD at QTL-ple5A, QTL-ple7A.1 and QTL-ple7B.1 region. Further selective sweep analysis revealled that regions under selection were around QTLs for these traits. Especially, grain yield (GY) is positively correlated with MD/FP and they were co-located at the VRN-1A locus. Besides, a selective sweep signal was detected at VRN-1B locus which was only significance to MD/FP. CONCLUSIONS: The results indicated that extensive differential in allele frequency driven by ecological selection has shaped plant architecture and growing season during yield improvement. The QTLs for yield and yield components detected in this study probably be selectively applied in molecular breeding.

Molecular characterization of a novel TaGL3-5A allele and its association with grain length in wheat (Triticum aestivum L.).

KEY MESSAGE: We isolated a novel allele associated with grain length and grain weight in wheat, TaGL3-5A-G. The TaGL3-5A-G allele frequency is low in wheat, so it has potential for breeding. Selection of large-grain wheat showing big grain sink potential and strong sink activity is becoming an important objective in breeding programs. Here, we cloned a wheat TaGL3-5A gene that was orthologous to rice GL3 and was phylogenetically clustered with both monocot PPKL1 and its expression pattern was similar to grain size change at early and middle stages of seed development. The isolated TaGL3-5A genomic sequence was 10,227 bp long and included 21 exons and 20 introns. Alignment of the TaGL3-5A sequences in Beinong 6 and Yanda 1817 showed a G/A substitution in the 11th exon (position 5946) that would lead to an amino acid change (Met/Ile). Subsequently, a KASP marker was designed based on this SNP. Genotyping of RILs showed that TaGL3-5A was located on the wheat 5AL chromosome and was colocated with a significant grain length QTL in three independent environments and mean value. Association analysis revealed that the TaGL3-5A-G allele was significantly correlated with longer grains and higher thousand-kernel weight. Haplotype association analysis indicated that TaGL3-5A-G could enhance grain traits in combination with TaGS5-3A and TaGW2-6B. The frequency of TaGL3-5A-G was higher in modern cultivars than in landraces but was still low in major Chinese wheat production areas. Additionally, the frequency of the TaGL3-5A-G allele in hexaploid wheat was slightly lower than in Triticum dicoccoides and much lower than in Triticum turgidum. Hence, T. dicoccoides and T. turgidum represent valuable resources for transferring the TaGL3-5A-G allele into common wheat, which should lead to longer grain length.

Cloning, characterization of TaGS3 and identification of allelic variation associated with kernel traits in wheat (Triticum aestivum L.).

BACKGROUND: Grain weight is an important yield component. Selection of advanced lines with heavy grains show high grain sink potentials and strong sink activity, which is an increasingly important objective in wheat breeding programs. Rice OsGS3 has been identified as a major quantitative trait locus for both grain weight and grain size. However, allelic variation of GS3 has not been characterized previously in hexaploid wheat. RESULTS: We cloned 2445, 2393, and 2409 bp sequences of the homologs TaGS3-4A, TaGS3-7A, and TaGS3-7D in wheat 'Changzhi 6406', a cultivar that shows high grain weight. The TaGS3 genes each contained five exons and four introns, and encoded a deduced protein of 170, 169, and 169 amino acids, respectively. Phylogenetic analysis of plant GS3 protein sequences revealed GS3 to be a monocotyledon-specific gene and the GS3 proteins were resolved into three classes. The length of the atypical Gγ domain and the cysteine-rich region was conserved within each class and not conserved between classes. A single-nucleotide polymorphism in the fifth exon (at position 1907) of TaGS3-7A leads to an amino acid change (ALA/THR) and showed different frequencies in two pools of Chinese wheat accessions representing extremes in grain weight. Association analysis indicated that the TaGS3-7A-A allele was associated with higher grain weight in the natural population. The TaGS3-7A-A allele was favoured in global modern wheat cultivars but the allelic frequency varied among different wheat-production regions of China, which indicated that this allele is of potential utility to improve wheat grain weight in certain wheat-production areas of China. CONCLUSIONS: The novel molecular information on wheat GS3 homologs and the KASP functional marker designed in this study may be useful in marker-assisted breeding for genetic improvement of wheat.

Mapping stripe rust resistance gene YrZH22 in Chinese wheat cultivar Zhoumai 22 by bulked segregant RNA-Seq (BSR-Seq) and comparative genomics analyses.

KEY MESSAGE: A stripe rust resistance gene YrZH22 was mapped by combined BSR-Seq and comparative genomics analyses to a 5.92 centimorgan (cM) genetic interval spanning a 4 Mb physical genomic region on wheat chromosome 4BL1. Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most destructive diseases of wheat and severely threatens wheat production worldwide. The widely grown Chinese wheat cultivar Zhoumai 22 is highly resistant to the current prevailing PST race CYR34 (V26). Genetic analysis of F5:6 and F6:7 recombinant inbred line (RIL) populations indicated that adult-plant stripe rust resistance in Zhoumai 22 is controlled by a single gene, temporarily designated YrZH22. By applying bulked segregant RNA-Seq (BSR-Seq), 7 SNP markers were developed and SNP mapping showed that YrZH22 is located between markers WGGB105 and WGGB112 on chromosome arm 4BL. The corresponding genomic regions of the Chinese Spring 4BL genome assembly and physical map of Aegilops tauschii 4DL were selected for comparative genomics analyses to develop nine new polymorphic markers that were used to construct a high-resolution genetic linkage map of YrZH22. YrZH22 was delimited in a 5.92 cM genetic interval between markers WGGB133 and WGGB146, corresponding to 4.1 Mb genomic interval in Chinese Spring 4BL and a 2.2 Mb orthologous genomic region in Ae. tauschii 4DL. The genetic linkage map of YrZH22 will be valuable for fine mapping and positional cloning of YrZH22, and can be used for marker-assisted selection in wheat breeding.