Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield

Genome-editing of a circadian clock gene TaPRR95 facilitates wheat peduncle growth and heading date

Plant height and heading date are important agronomic traits in wheat (Triticum aestivum L.) that affect final grain yield. In wheat, knowledge of pseudo-response regulator (PRR) genes on agronomic traits is limited. Here, we identify a wheat TaPRR95 gene by genome-wide association study (GWAS) to be associated with plant height. Triple allele mutant plants produced by CRISPR/Cas9 show increased plant height, particularly at the peduncle, with an earlier heading date. The longer peduncle is mainly caused by the increased cell elongation at its upper section, whilst the early heading date is accompanied with elevated expression of flowering genes, such as TaFT and TaCO1. A peduncle-specific transcriptome analysis reveals up-regulated photosynthesis genes and down-regulated IAA/Aux genes for auxin signaling in prr95aabbdd plants that may act as a regulatory mechanism to promote robust plant growth. A haplotype analysis identifies a TaPRR95-B haplotype (Hap2) to be closely associated with reduced plant height and increased thousand-grain weight. Moreover, the Hap2 frequency is higher in cultivars than that in landraces, suggesting the artificial selection on the allele during wheat breeding. These findings suggest that TaPRR95 is a new regulator for plant height and heading date, thereby providing an important target for wheat yield improvement.

Identification and validation of two major QTL for grain number per spike on chromosomes 2B and 2D in bread wheat (Triticum aestivum L.)

KEY MESSAGE

Major QTL for grain number per spike were identified on chromosomes 2B and 2D. Haplotypes and candidate genes of QGns.cib-2B.1 were analyzed. Grain number per spike (GNS) is one of the main components of wheat yield. Genetic dissection of their regulatory factors is essential to improve the yield potential. In present study, a recombinant inbred line population comprising 180 lines developed from the cross between a high GNS line W7268 and a cultivar Chuanyu12 was employed to identify quantitative trait loci (QTL) associated with GNS across six environments. Two major QTL, QGns.cib-2B.1 and QGns.cib-2D.1, were detected in at least four environments with the phenotypic variations of 12.99-27.07% and 8.50-13.79%, respectively. And significant interactions were observed between the two major QTL. In addition, QGns.cib-2B.1 is a QTL cluster for GNS, grain number per spikelet and fertile tiller number, and they were validated in different genetic backgrounds using Kompetitive Allele Specific PCR (KASP) markers. QGns.cib-2B.1 showed pleotropic effects on other yield-related traits including plant height, spike length, and spikelet number per spike, but did not significantly affect thousand grain weight which suggested that it might be potentially applicable in breeding program. Comparison analysis suggested that QGns.cib-2B.1 might be a novel QTL. Furthermore, haplotype analysis of QGns.cib-2B.1 indicated that it is a hot spot of artificial selection during wheat improvement. Based on the expression patterns, gene annotation, orthologs analysis and sequence variations, the candidate genes of QGns.cib-2B.1 were predicted. Collectively, the major QTL and KASP markers reported here provided a wealth of information for the genetic basis of GNS and grain yield improvement.

Effects and molecular mechanisms of polyethylene microplastic oxidation on wheat grain quality

Polyethylene microplastics (PE MPs) are the main MPs in agricultural soils and undergo oxidation upon environmental exposure. However, the influence of MP oxidation on phytotoxicity (especially for crop fruit) is still limited. This study aimed to explore the effect of PE MP oxidation on crop toxicity. Herein, a combination of plant phenotyping, metabolomic, and transcriptomic approaches was used to evaluate the effects of low-oxidation PE (LOPE) and high-oxidation PE (HOPE) on wheat growth, grain quality, and related molecular mechanisms using pot experiments. The results showed that HOPE induced a stronger inhibition of wheat growth and reduction in protein content and mineral elements than LOPE. This was accompanied by root ultrastructural damage and downregulation of carbohydrate metabolism, translation, nutrient reservoir activity, and metal ion binding gene expression. Compared with HOPE, LOPE activated a stronger plant defense response by reducing the starch content by 22.87 %, increasing soluble sugar content by 44.93 %, and upregulating antioxidant enzyme genes and crucial metabolic pathways (e.g., starch and sucrose, linoleic acid, and phenylalanine metabolism). The presence of PE MPs in the environment exacerbates crop growth inhibition and fruit quality deterioration, highlighting the need to consider the environmental and food safety implications of MPs in agricultural soils.

Genomic insights into glume pubescence in durum wheat: GWAS and haplotype analysis implicates TdELD1-1A as a candidate gene

Glume pubescence is an important morphological trait for the characterization of wheat cultivars. It shows tolerance to biotic and abiotic stresses to some extent. Hg1 (formerly named Hg) locus on chromosome 1AS controls glume pubescence in wheat. Its genetic analysis, fine-mapping and candidate gene analysis have been widely studied recently, however, the cloning of Hg1 has not yet been reported. Here, we conducted a GWAS between a dense panel of 171,103 SNPs and glume pubescence (Gp) in a durum wheat population of 145 lines, and further analyzed the candidate genes of Hg1 combined with the gene expression, functional annotation, and haplotype analysis. As a results, TRITD0Uv1G104670 (TdELD1-1A), encoding glycosyltransferase-like ELD1/KOBITO 1, was detected as the most promising candidate gene of Hg1 for glume pubescence in durum wheat. Our findings not only contribute to a deeper understanding of its cloning and functional validation but also underscore the significance of accurate genome sequences and annotations. Additionally, our study highlights the relevance of unanchored sequences in chrUn and the application of bioinformatics analysis for gene discovery in durum wheat.

Pleiotropic phenotypic effects of the TaCYP78A family on multiple yield-related traits in wheat

Increasing crop yield depends on selecting and utilizing pleiotropic genes/alleles to improve multiple yield-related traits (YRTs) during crop breeding. However, synergistic improvement of YRTs is challenging due to the trade-offs between YRTs in breeding practices. Here, the favourable haplotypes of the TaCYP78A family are identified by analysing allelic variations in 1571 wheat accessions worldwide, demonstrating the selection and utilization of pleiotropic genes to improve yield and related traits during wheat breeding. The TaCYP78A family members, including TaCYP78A3, TaCYP78A5, TaCYP78A16, and TaCYP78A17, are organ size regulators expressed in multiple organs, and their allelic variations associated with various YRTs. However, due to the trade-offs between YRTs, knockdown or overexpression of TaCYP78A family members does not directly increase yield. Favourable haplotypes of the TaCYP78A family, namely A3/5/16/17Ap-Hap II, optimize the expression levels of TaCYP78A3/5/16/17-A across different wheat organs to overcome trade-offs and improve multiple YRTs. Different favourable haplotypes have both complementary and specific functions in improving YRTs, and their aggregation in cultivars under strong artificial selection greatly increase yield, even under various planting environments and densities. These findings provide new support and valuable genetic resources for molecular breeding of wheat and other crops in the era of Breeding 4.0.

Genome-wide association study for seedling heat tolerance under two temperature conditions in bread wheat (Triticum aestivum L.)

BACKGROUND

As the greenhouse effect intensifies, global temperatures are steadily increasing, posing a challenge to bread wheat (Triticum aestivum L.) production. It is imperative to comprehend the mechanism of high temperature tolerance in wheat and implement breeding programs to identify and develop heat-tolerant wheat germplasm and cultivars.

RESULTS

To identify quantitative trait loci (QTL) related to heat stress tolerance (HST) at seedling stage in wheat, a panel of 253 wheat accessions which were re-sequenced used to conduct genome-wide association studies (GWAS) using the factored spectrally transformed linear mixed models (FaST-LMM). For most accessions, the growth of seedlings was found to be inhibited under heat stress. Analysis of the phenotypic data revealed that under heat stress conditions, the main root length, total root length, and shoot length of seedlings decreased by 47.46%, 49.29%, and 15.19%, respectively, compared to those in normal conditions. However, 17 varieties were identified as heat stress tolerant germplasm. Through GWAS analysis, a total of 115 QTLs were detected under both heat stress and normal conditions. Furthermore, 15 stable QTL-clusters associated with heat response were identified. By combining gene expression, haplotype analysis, and gene annotation information within the physical intervals of the 15 QTL-clusters, two novel candidate genes, TraesCS4B03G0152700/TaWRKY74-B and TraesCS4B03G0501400/TaSnRK3.15-B, were responsive to temperature and identified as potential regulators of HST in wheat at the seedling stage.

CONCLUSIONS

This study conducted a detailed genetic analysis and successfully identified two genes potentially associated with HST in wheat at the seedling stage, laying a foundation to further dissect the regulatory mechanism underlying HST in wheat under high temperature conditions. Our finding could serve as genomic landmarks for wheat breeding aimed at improving adaptation to heat stress in the face of climate change.

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.

Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat

Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits. Here, we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat. We identified 170 loci that are responsible for variations in spike length, spikelet number per spike, and grain number per spike through genome-wide association study and meta-QTL analyses. We constructed gene regulatory networks for young inflorescences at the double ridge stage and the floret primordium stage, in which the spikelet meristem and the floret meristem are predominant, respectively, by integrating transcriptome, histone modification, chromatin accessibility, eQTL, and protein-protein interactome data. From these networks, we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits. The functions of TaZF-B1, VRT-B2, and TaSPL15-A/D in establishment of wheat spike architecture were verified. This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.

Comprehensive Comparative Analysis of the JAZ Gene Family in Common Wheat (Triticum aestivum) and Its D-Subgenome Donor Aegilops tauschii

JASMONATE-ZIM DOMAIN (JAZ) repressor proteins work as co-receptors in the jasmonic acid (JA) signalling pathway and are essential for plant development and environmental adaptation. Despite wheat being one of the main staple food crops, until recently, comprehensive analysis of its JAZ gene family has been limited due to the lack of complete and high-quality reference genomes. Here, using the latest reference genome, we identified 17 JAZ genes in the wheat D-genome donor Aegilops tauschii. Then, 54 TaJAZs were identified in common wheat. A systematic examination of the gene structures, conserved protein domains, and phylogenetic relationships of this gene family was performed. Five new JAZ genes were identified as being derived from tandem duplication after wheat divergence from other species. We integrated RNA-seq data and yield QTL information and found that tandemly duplicated TaJAZ genes were prone to association with spike-related traits. Moreover, 12 TaJAZ genes were located within breeding selection sweeps, including 9 tandemly duplicated ones. Haplotype variation analysis of selected JAZ genes showed significant association of TaJAZ7A and TaJAZ13A with thousand-grain weight. Our work provides a clearer picture of wheat JAZ gene evolution and puts forward the possibility of using these genes for wheat yield improvement.

Reviewing the essential roles of remote phenotyping, GWAS and explainable AI in practical marker-assisted selection for drought-tolerant winter wheat breeding

Marker-assisted selection (MAS) plays a crucial role in crop breeding improving the speed and precision of conventional breeding programmes by quickly and reliably identifying and selecting plants with desired traits. However, the efficacy of MAS depends on several prerequisites, with precise phenotyping being a key aspect of any plant breeding programme. Recent advancements in high-throughput remote phenotyping, facilitated by unmanned aerial vehicles coupled to machine learning, offer a non-destructive and efficient alternative to traditional, time-consuming, and labour-intensive methods. Furthermore, MAS relies on knowledge of marker-trait associations, commonly obtained through genome-wide association studies (GWAS), to understand complex traits such as drought tolerance, including yield components and phenology. However, GWAS has limitations that artificial intelligence (AI) has been shown to partially overcome. Additionally, AI and its explainable variants, which ensure transparency and interpretability, are increasingly being used as recognised problem-solving tools throughout the breeding process. Given these rapid technological advancements, this review provides an overview of state-of-the-art methods and processes underlying each MAS, from phenotyping, genotyping and association analyses to the integration of explainable AI along the entire workflow. In this context, we specifically address the challenges and importance of breeding winter wheat for greater drought tolerance with stable yields, as regional droughts during critical developmental stages pose a threat to winter wheat production. Finally, we explore the transition from scientific progress to practical implementation and discuss ways to bridge the gap between cutting-edge developments and breeders, expediting MAS-based winter wheat breeding for drought tolerance.

A nonsynonymous mutation in BhLS, encoding an acyl-CoA N-acyltransferase leads to fruit and seed size variation in wax gourd (Benincasa hispida)

Wax gourd (Benincasa hispida (Thunb.) Cogn., 2n = 2x = 24) is an economically important vegetable crop cultivated widely in many tropical and subtropical regions, including China, India, and Japan. Both fruit and seeds are prized agronomic attributes in wax gourd breeding and production. However, the genetic mechanisms underlying these traits remain largely unexplored. In this study, we observed a strong correlation between fruit size and seed size variation in our mapping population, indicating genetic control by a single gene, BhLS, with large size being dominant over small. Through bulk segregant analysis sequencing and fine mapping with a large F2 population, we precisely located the BhLS gene within a 47.098-kb physical interval on Chromosome 10. Within this interval, only one gene, Bhi10M000649, was identified, showing homology to Arabidopsis HOOKLESS1. A nonsynonymous mutation (G to C) in the second exon of Bhi10M000649 was found to be significantly associated with both fruit and seed size variation in wax gourd. These findings collectively highlight the pleiotropic effect of the BhLS gene in regulating fruit and seed size in wax gourd. Our results offer molecular insights into the variation of fruit and seed size in wax gourd and establish a fundamental framework for breeding wax gourd cultivars with desired traits.

Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm

A panel comprising of 84 Turkish winter wheat landraces (LR) and 73 modern varieties (MV) was analyzed with genome wide association study (GWAS) to identify genes/genomic regions associated with increased yield under favorable and drought conditions. In addition, selective sweep analysis was conducted to detect signatures of selection in the winter wheat genome driving the differentiation between LR and MV, to gather an understanding of genomic regions linked to adaptation and yield improvement. The panel was genotyped with 25 K wheat SNP array and phenotyped for agronomic traits for two growing seasons (2018 and 2019) in Konya, Turkey. Year 2018 was treated as drought environment due to very low precipitation prior to heading whereas year 2019 was considered as a favorable season. GWAS conducted with SNPs and haplotype blocks using mixed linear model identified 18 genomic regions in the vicinities of known genes i.e., TaERF3-3A, TaERF3-3B, DEP1-5A, FRIZZY PANICLE-2D, TaSnRK23-1A, TaAGL6-A, TaARF12-2A, TaARF12-2B, WAPO1, TaSPL16-7D, TaTGW6-A1, KAT-2B, TaOGT1, TaSPL21-6B, TaSBEIb, trs1/WFZP-A, TaCwi-A1-2A and TaPIN1-7A associated with grain yield (GY) and yield related traits. Haplotype-based GWAS identified five haplotype blocks (H1A-42, H2A-71, H4A-48, H7B-123 and H7B-124), with the favorable haplotypes showing a yield increase of > 700 kg/ha in the drought season. SNP-based GWAS, detected only one larger effect genomic region on chromosome 7B, in common with haplotype-based GWAS. On an average, the percentage variation (PV) explained by haplotypes was 8.0% higher than PV explained by SNPs for all the investigated traits. Selective sweep analysis detected 39 signatures of selection between LR and MV of which 15 were within proximity of known functional genes controlling flowering (PRR-A1, PPR-D1, TaHd1-6B), GY and GY components (TaSus2-2B, TaGS2-B1, AG1-1A/WAG1-1A, DUO-A1, DUO-B1, AG2-3A/WAG2-3A, TaLAX1, TaSnRK210-4A, FBP, TaLAX1, TaPIL1 and AP3-1-7A/WPA3-7A) and 10 regions underlying various transcription factors and regulatory genes. The study outcomes contribute to utilization of LR in breeding winter wheat.

Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses

The spike architecture of wheat plays a crucial role in determining grain number, making it a key trait for optimization in wheat breeding programs. In this study, we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages, revealing coordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition. We constructed a core transcriptional regulatory network (TRN) that drives wheat spike formation and experimentally validated a multi-layer regulatory module involving TaSPL15, TaAGLG1, and TaFUL2. By integrating the TRN with genome-wide association studies, we identified 227 transcription factors, including 42 with known functions and 185 with unknown functions. Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time, such as TaMYC2-A1, TaMYB30-A1, and TaWRKY37-A1. Of particular interest, TaMYB30-A1, downstream of and repressed by WFZP, was found to regulate fertile spikelet number. Notably, the excellent haplotype of TaMYB30-A1, which contains a C allele at the WFZP binding site, was enriched during wheat breeding improvement in China, leading to improved agronomic traits. Finally, we constructed a free and open access Wheat Spike Multi-Omic Database (http://39.98.48.156:8800/#/). Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development, with practical value for wheat breeding.

Genome-wide association studies reveal stable loci for wheat grain size under different sowing dates

Background

Wheat (Tritium aestivum L.) production is critical for global food security. In recent years, due to climate change and the prolonged growing period of rice varieties, the delayed sowing of wheat has resulted in a loss of grain yield in the area of the middle and lower reaches of the Yangtze River. It is of great significance to screen for natural germplasm resources of wheat that are resistant to late sowing and to explore genetic loci that stably control grain size and yield.

Methods

A collection of 327 wheat accessions from diverse sources were subjected to genome-wide association studies using genotyping-by-sequencing. Field trials were conducted under normal, delayed, and seriously delayed sowing conditions for grain length, width, and thousand-grain weight at two sites. Additionally, the additive main effects and multiplicative interaction (AMMI) model was applied to evaluate the stability of thousand-grain weight of 327 accessions across multiple sowing dates.

Results

Four wheat germplasm resources have been screened, demonstrating higher stability of thousand-grain weight. A total of 43, 35, and 39 significant MTAs were determined across all chromosomes except for 4D under the three sowing dates, respectively. A total of 10.31% of MTAs that stably affect wheat grain size could be repeatedly identified in at least two sowing dates, with PVE ranging from 0.03% to 38.06%. Among these, six were for GL, three for GW, and one for TGW. There were three novel and stable loci (4A_598189950, 4B_307707920, 2D_622241054) located in conserved regions of the genome, which provide excellent genetic resources for pyramid breeding strategies of superior loci. Our findings offer a theoretical basis for cultivar improvement and marker-assisted selection in wheat breeding practices.

Genetic dissection of major QTL for grain number per spike on chromosomes 5A and 6A in bread wheat (Triticum aestivum L.)

Grain number per spike (GNS) is a crucial component of grain yield and plays a significant role in improving wheat yield. To identify quantitative trait loci (QTL) associated with GNS, a recombinant inbred line (RIL) population derived from the cross of Zhongkemai 13F10 and Chuanmai 42 was employed to conduct QTL mapping across eight environments. Based on the bulked segregant exome sequencing (BSE-Seq), genomic regions associated with GNS were detected on chromosomes 5A and 6A. According to the constructed genetic maps, two major QTL QGns.cib-5A (LOD = 4.35-8.16, PVE = 8.46-14.43%) and QGns.cib-6A (LOD = 3.82-30.80, PVE = 5.44-12.38%) were detected in five and four environments, respectively. QGns.cib-6A is a QTL cluster for other seven yield-related traits. QGns.cib-5A and QGns.cib-6A were further validated using linked Kompetitive Allele Specific PCR (KASP) markers in different genetic backgrounds. QGns.cib-5A exhibited pleiotropic effects on productive tiller number (PTN), spike length (SL), fertile spikelet number per spike (FSN), and ratio of grain length to grain width (GL/GW) but did not significantly affect thousand grain weight (TGW). Haplotype analysis revealed that QGns.cib-5A and QGns.cib-6A were the targets of artificial selection during wheat improvement. Candidate genes for QGns.cib-5A and QGns.cib-6A were predicted by analyzing gene annotation, spatiotemporal expression patterns, and orthologous and sequence differences. These findings will be valuable for fine mapping and map-based cloning of genes underlying QGns.cib-5A and QGns.cib-6A.

Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement

Despite recent progress in crop genomics studies, the genomic changes brought about by modern breeding selection are still poorly understood, thus hampering genomics-assisted breeding, especially in polyploid crops with compound genomes such as common wheat (Triticum aestivum). In this work, we constructed genome resources for the modern elite common wheat variety Aikang 58 (AK58). Comparative genomics between AK58 and the landrace cultivar Chinese Spring (CS) shed light on genomic changes that occurred through recent varietal improvement. We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study (HGWAS) approach, which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci. A total of 123 major HGWAS loci were detected using a genetic population derived from AK58 and CS. Elite homoeologous haplotypes (HHs), formed by combinations of subgenomic homoeologs of the associated loci, were found in both parents and progeny, and many could substantially improve wheat yield and related traits. We built a website where users can download genome assembly sequence and annotation data for AK58, perform blast analysis, and run JBrowse. Our work enriches genome resources for wheat, provides new insights into genomic changes during modern wheat improvement, and suggests that efficient mining of elite HHs can make a substantial contribution to genomics-assisted breeding in common wheat and other polyploid crops.

Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States

Breeding has dramatically changed the plant architecture of wheat (Triticum aestivum), resulting in the development of high-yielding varieties adapted to modern farming systems. However, how wheat breeding shaped the genomic architecture of this crop remains poorly understood. Here, we performed a comprehensive comparative analysis of a whole-genome resequencing panel of 355 common wheat accessions (representing diverse landraces and modern cultivars from China and the United States) at the phenotypic and genomic levels. The genetic diversity of modern wheat cultivars was clearly reduced compared to landraces. Consistent with these genetic changes, most phenotypes of cultivars from China and the United States were significantly altered. Of the 21 agronomic traits investigated, 8 showed convergent changes between the 2 countries. Moreover, of the 207 loci associated with these 21 traits, more than half overlapped with genomic regions that showed evidence of selection. The distribution of selected loci between the Chinese and American cultivars suggests that breeding for increased productivity in these 2 regions was accomplished by pyramiding both shared and region-specific variants. This work provides a framework to understand the genetic architecture of the adaptation of wheat to diverse agricultural production environments, as well as guidelines for optimizing breeding strategies to design better wheat varieties.

Deciphering the evolution and complexity of wheat germplasm from a genomic perspective

Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.

Two QTL regions for spike length showing pleiotropic effects on Fusarium head blight resistance and thousand-grain weight in bread wheat (Triticum aestivum L.)

Spike length (SL) plays an important role in the yield improvement of wheat and is significantly associated with other traits. Here, we used a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) to construct a genetic linkage map and identify quantitative trait loci (QTL) for SL. A total of 5 QTL were identified for SL, among which QSl.yaas-3A and QSl.yaas-5B are two novel QTL for SL. The YZ1 alleles at QSl.yaas-2D and QSl.yaas-5A, and the YM12 alleles at QSl.yaas-2A, QSl.yaas-3A, and QSl.yaas-5B conferred increasing SL effects. Two major QTL QSl.yaas-5A and QSl.yaas-5B explained 9.11-15.85% and 9.01-12.85% of the phenotypic variations, respectively. Moreover, the positive alleles of QSl.yaas-5A and QSl.yaas-5B could significantly increase Fusarium head blight (FHB) resistance (soil surface inoculation and spray inoculation were used) and thousand-grain weight (TGW) in the RIL population. Kompetitive allele-specific PCR (KASP) markers for QSl.yaas-5A and QSl.yaas-5B were developed and validated in an additional panel of 180 wheat cultivars/lines. The cultivars/lines harboring both the positive alleles of QSl.yaas-5A and QSl.yaas-5B accounted for only 28.33% of the validation populations and had the longest SL, best FHB resistance (using spray inoculation), and highest TGW. A total of 358 and 200 high-confidence annotated genes in QSl.yaas-5A and QSl.yaas-5B were identified, respectively. Some of the genes in these two regions were involved in cell development, disease resistance, and so on. The results of this study will provide a basis for directional breeding of longer SL, higher TGW, and better FHB resistance varieties and a solid foundation for fine-mapping QSl.yaas-5A and QSl.yaas-5B in future.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01427-8.

Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Gossypium hirsutum L.)

Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.

Grain yield improvement by genome editing of TaARF12 that decoupled peduncle and rachis development trajectories via differential regulation of gibberellin signalling in wheat

Plant breeding is constrained by trade-offs among different agronomic traits by the pleiotropic nature of many genes. Genes that contribute to two or more favourable traits with no penalty on yield are rarely reported, especially in wheat. Here, we describe the editing of a wheat auxin response factor TaARF12 by using CRISPR/Cas9 that rendered shorter plant height with larger spikes. Changes in plant architecture enhanced grain number per spike up to 14.7% with significantly higher thousand-grain weight and up to 11.1% of yield increase under field trials. Weighted Gene Co-Expression Network Analysis (WGCNA) of spatial-temporal transcriptome profiles revealed two hub genes: RhtL1, a DELLA domain-free Rht-1 paralog, which was up-regulated in peduncle, and TaNGR5, an organ size regulator that was up-regulated in rachis, in taarf12 plants. The up-regulation of RhtL1 in peduncle suggested the repression of GA signalling, whereas up-regulation of TaNGR5 in spike may promote GA response, a working model supported by differential expression patterns of GA biogenesis genes in the two tissues. Thus, TaARF12 complemented plant height reduction with larger spikes that gave higher grain yield. Manipulation of TaARF12 may represent a new strategy in trait pyramiding for yield improvement in wheat.

Identification and Molecular Mapping of the Gene YrFL in Wheat Cultivar Flanders with Durable Resistance to Stripe Rust

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most severe diseases of wheat (Triticum aestivum L.) worldwide. Identification and characterization of resistance genes is advantageous to cultivating wheat varieties with durable resistance, which is the most economic and effective strategy to control stripe rust. Flanders, a common wheat cultivar released in France in 1986, confers effective resistance to stripe rust both at the seedling and adult plant stages. To elucidate the genetic basis of resistance in Flanders, F1, F2, and F2:3 generations derived from the cross Mingxian169 × Flanders were evaluated with the most prevalent Chinese Pst race CYR33 at the seedling stage. Inheritance analysis showed that the stripe rust resistance of Flanders was controlled by a single dominant gene, temporarily designated as YrFL. Bulked segregant analysis (BSA) combined with a wheat 660K single-nucleotide polymorphism (SNP) array indicated that polymorphic SNP markers were mainly located in the 0 to 150 Mb on wheat chromosome 5A. One hundred and eleven kompetitive allele-specific PCR (KASP) and 39 simple sequence repeat (SSR) markers on chromosome 5A were used to locate the YrFL. Linkage analysis mapped YrFL with 19 KASP and three SSR markers on wheat chromosome 5AS, and the genetic distances of the closest flanking markers AX108925494 and Xbarc56 to YrFL were 0.6 and 2.0 cM, respectively. Chromosome location, resistance characterization, and molecular marker positions indicated that YrFL is likely a novel stripe rust resistance gene on wheat chromosome 5AS and could be pyramided with other resistance genes to improve resistance in wheat breeding programs.

The Genetic Structures and Molecular Mechanisms Underlying Ear Traits in Maize (Zea mays L.)

Maize (Zea mays L.) is one of the world's staple food crops. In order to feed the growing world population, improving maize yield is a top priority for breeding programs. Ear traits are important determinants of maize yield, and are mostly quantitatively inherited. To date, many studies relating to the genetic and molecular dissection of ear traits have been performed; therefore, we explored the genetic loci of the ear traits that were previously discovered in the genome-wide association study (GWAS) and quantitative trait locus (QTL) mapping studies, and refined 153 QTL and 85 quantitative trait nucleotide (QTN) clusters. Next, we shortlisted 19 common intervals (CIs) that can be detected simultaneously by both QTL mapping and GWAS, and 40 CIs that have pleiotropic effects on ear traits. Further, we predicted the best possible candidate genes from 71 QTL and 25 QTN clusters that could be valuable for maize yield improvement.

Genome wide association and haplotype analyses for the crease depth trait in bread wheat (Triticum aestivum L.)

Wheat grain has a complex structure that includes a crease on one side, and tissues within the crease region play an important role in nutrient transportation during wheat grain development. However, the genetic architecture of the crease region is still unclear. In this study, 413 global wheat accessions were resequenced and a method was developed for evaluating the phenotypic data of crease depth (CD). The CD values exhibited continuous and considerable large variation in the population, and the broad-sense heritability was 84.09%. CD was found to be positively correlated with grain-related traits and negatively with quality-related traits. Analysis of differentiation of traits between landraces and cultivars revealed that grain-related traits and CD were simultaneously improved during breeding improvement. Moreover, 2,150.8-Mb genetic segments were identified to fall within the selective sweeps between the landraces and cultivars; they contained some known functional genes for quality- and grain-related traits. Genome-wide association study (GWAS) was performed using around 10 million SNPs generated by genome resequencing and 551 significant SNPs and 18 QTLs were detected significantly associated with CD. Combined with cluster analysis of gene expression, haplotype analysis, and annotated information of candidate genes, two promising genes TraesCS3D02G197700 and TraesCS5A02G292900 were identified to potentially regulate CD. To the best of our knowledge, this is the first study to provide the genetic basis of CD, and the genetic loci identified in this study may ultimately assist in wheat breeding programs.

TaTPP-7A positively feedback regulates grain filling and wheat grain yield through T6P-SnRK1 signalling pathway and sugar-ABA interaction

Grain size and filling are two key determinants of grain thousand-kernel weight (TKW) and crop yield, therefore they have undergone strong selection since cereal was domesticated. Genetic dissection of the two traits will improve yield potential in crops. A quantitative trait locus significantly associated with wheat grain TKW was detected on chromosome 7AS flanked by a simple sequence repeat marker of Wmc17 in Chinese wheat 262 mini-core collection by genome-wide association study. Combined with the bulked segregant RNA-sequencing (BSR-seq) analysis of an F₂ genetic segregation population with extremely different TKW traits, a candidate trehalose-6-phosphate phosphatase gene located at 135.0 Mb (CS V1.0), designated as TaTPP-7A, was identified. This gene was specifically expressed in developing grains and strongly influenced grain filling and size. Overexpression (OE) of TaTPP-7A in wheat enhanced grain TKW and wheat yield greatly. Detailed analysis revealed that OE of TaTPP-7A significantly increased the expression levels of starch synthesis- and senescence-related genes involved in abscisic acid (ABA) and ethylene pathways. Moreover, most of the sucrose metabolism and starch regulation-related genes were potentially regulated by SnRK1. In addition, TaTPP-7A is a crucial domestication- and breeding-targeted gene and it feedback regulates sucrose lysis, flux, and utilization in the grain endosperm mainly through the T6P-SnRK1 pathway and sugar-ABA interaction. Thus, we confirmed the T6P signalling pathway as the central regulatory system for sucrose allocation and source-sink interactions in wheat grains and propose that the trehalose pathway components have great potential to increase yields in cereal crops.

Genetic basis of geographical differentiation and breeding selection for wheat plant architecture traits

BACKGROUND

Plant architecture associated with increased grain yield and adaptation to the local environments is selected during wheat (Triticum aestivum) breeding. The internode length of individual stems and tiller length of individual plants are important for the determination of plant architecture. However, few studies have explored the genetic basis of these traits.

RESULTS

Here, we conduct a genome-wide association study (GWAS) to dissect the genetic basis of geographical differentiation of these traits in 306 worldwide wheat accessions including both landraces and traditional varieties. We determine the changes of haplotypes for the associated genomic regions in frequency in 831 wheat accessions that are either introduced from other countries or developed in China from last two decades. We identify 83 loci that are associated with one trait, while the remaining 247 loci are pleiotropic. We also find 163 associated loci are under strong selective sweep. GWAS results demonstrate independent regulation of internode length of individual stems and consistent regulation of tiller length of individual plants. This makes it possible to obtain ideal haplotype combinations of the length of four internodes. We also find that the geographical distribution of the haplotypes explains the observed differences in internode length among the worldwide wheat accessions.

CONCLUSION

This study provides insights into the genetic basis of plant architecture. It will facilitate gene functional analysis and molecular design of plant architecture for breeding.

Variations in phenological, physiological, plant architectural and yield-related traits, their associations with grain yield and genetic basis

BACKGROUND AND AIMS

Physiological and morphological traits play essential roles in wheat (Triticum aestivum) growth and development. In particular, photosynthesis is a limitation to yield. Increasing photosynthesis in wheat has been identified as an important strategy to increase yield. However, the genotypic variations and the genomic regions governing morphological, architectural and photosynthesis traits remain unexplored.

METHODS

Here, we conducted a large-scale investigation of the phenological, physiological, plant architectural and yield-related traits, involving 32 traits for 166 wheat lines during 2018-2020 in four environments, and performed a genome-wide association study with wheat 90K and 660K single nucleotide polymorphism (SNP) arrays.

KEY RESULTS

These traits exhibited considerable genotypic variations in the wheat diversity panel. Higher yield was associated with higher net photosynthetic rate (r = 0.41, P < 0.01), thousand-grain weight (r = 0.36, P < 0.01) and truncated and lanceolate shape, but shorter plant height (r = -0.63, P < 0.01), flag leaf angle (r = -0.49, P < 0.01) and spike number per square metre (r = -0.22, P < 0.01). Genome-wide association mapping discovered 1236 significant stable loci detected in the four environments among the 32 traits using SNP markers. Trait values have a cumulative effect as the number of the favourable alleles increases, and significant progress has been made in determining phenotypic values and favourable alleles over the years. Eleven elite cultivars and 14 traits associated with grain yield per plot (GY) were identified as potential parental lines and as target traits to develop high-yielding cultivars.

CONCLUSIONS

This study provides new insights into the phenotypic and genetic elucidation of physiological and morphological traits in wheat and their associations with GY, paving the way for discovering their underlying gene control and for developing enhanced ideotypes in wheat breeding.

Genomic insights into the genetic basis of cotton breeding in China

The excellent Upland cotton (Gossypium hirsutum) cultivars developed since 1949 have made a huge contribution to cotton production in China, the world's largest producer and consumer of cotton. However, the genetic and genomic basis for the improvements of these cotton cultivars remains largely unclear. In this study, we selected 16 Upland cotton cultivars with important historical status in Chinese cotton breeding and constructed a multiparent, advanced generation, intercross (MAGIC) population comprising 920 recombinant inbred lines. A genome-wide association study using the MAGIC population identified 54 genomic loci associated with lint yield and fiber quality. Of them, 25 (46.30%) pleiotropic genomic loci cause simultaneous changes of lint yield and/or fiber quality traits, revealing complex trade-offs and linkage drags in Upland cotton agronomic traits. Deep sequencing data of 11 introduced ancestor cultivars and publicly available resequencing datasets of 839 cultivars developed in China during the past 70 years were integrated to explore the historical distribution and origin of the elite or selected alleles. Interestingly, 85% of these elite alleles were selected and fixed from different American ancestors, consistent with cotton breeding practices in China. However, seven elite alleles of native origin that are responsible for Fusarium wilt resistance, early maturing, good-quality fiber, and other characteristics were not found in American ancestors but have greatly contributed to Chinese cotton breeding and wide cultivation. Taken together, these results provide a genetic basis for further improving cotton cultivars and reveal that the genetic composition of Chinese cotton cultivars is narrow and mainly derived from early introduced American varieties.

Field-measured canopy height may not be as accurate and heritable as believed: evidence from advanced 3D sensing

Canopy height (CH) is an important trait for crop breeding and production. The rapid development of 3D sensing technologies shed new light on high-throughput height measurement. However, a systematic comparison of the accuracy and heritability of different 3D sensing technologies is seriously lacking. Moreover, it is questionable whether the field-measured height is as reliable as believed. This study uncovered these issues by comparing traditional height measurement with four advanced 3D sensing technologies, including terrestrial laser scanning (TLS), backpack laser scanning (BLS), gantry laser scanning (GLS), and digital aerial photogrammetry (DAP). A total of 1920 plots covering 120 varieties were selected for comparison. Cross-comparisons of different data sources were performed to evaluate their performances in CH estimation concerning different CH, leaf area index (LAI), and growth stage (GS) groups. Results showed that 1) All 3D sensing data sources had high correlations with field measurement (r > 0.82), while the correlations between different 3D sensing data sources were even better (r > 0.87). 2) The prediction accuracy between different data sources decreased in subgroups of CH, LAI, and GS. 3) Canopy height showed high heritability from all datasets, and 3D sensing datasets had even higher heritability (H² = 0.79-0.89) than FM (field measurement) (H² = 0.77). Finally, outliers of different datasets are analyzed. The results provide novel insights into different methods for canopy height measurement that may ensure the high-quality application of this important trait.

Identification of structural variations related to drought tolerance in wheat (Triticum aestivum L.)

Structural variations are common in plant genomes, affecting meiotic recombination and distorted segregation in wheat. And presence/absence variations can significantly affect drought tolerance in wheat. Drought is a major abiotic stress limiting wheat production. Common wheat has a complex genome with three sub-genomes, which host large numbers of structural variations (SVs). SVs play critical roles in understanding the genetic contributions of plant domestication and phenotypic plasticity, but little is known about their genomic characteristics and their effects on drought tolerance. In the present study, high-resolution karyotypes of 180 doubled haploids (DHs) were developed. Signal polymorphisms between the parents involved with 8 presence-absence variations (PAVs) of tandem repeats (TR) distributed on the 7 (2A, 4A, 5A, 7A, 3B, 7B, and 2D) of 21 chromosomes. Among them, PAV on chromosome 2D showed distorted segregation, others transmit normal conforming to a 1:1 segregation ration in the population; and a PAVs recombination occurred on chromosome 2A. Association analysis of PAV and phenotypic traits under different water regimes, we found PAVs on chromosomes 4A, 5A, and 7B showed negative effect on grain length (GL) and grain width (GW); PAV.7A had opposite effect on grain thickness (GT) and spike length (SL), with the effect on traits differing under different water regimes. PAVs on linkage group 2A, 4A, 7A, 2D, and 7B associated with the drought tolerance coefficients (DTCs), and significant negative effect on drought resistance values (D values) were detected in PAV.7B. Additionally, quantitative trait loci (QTL) associated with phenotypic traits using the 90 K SNP array showed QTL for DTCs and grain-related traits in chromosomes 4A, and 5A, 3B were co-localized in differential regions of PAVs. These PAVs can cause the differentiation of the target region of SNP and could be used for genetic improvement of agronomic traits under drought stress via marker-assisted selection (MAS) breeding.

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

The primary goal of modern wheat breeding is to develop new high-yielding and widely adaptable varieties. We analyzed four yield-related agronomic traits in 502 wheat accessions under normal conditions (NC) and drought treatment (DT) conditions over three years. The genome-wide association analysis identified 51 yield-related and nine drought-resistance-related QTL, including 13 for the thousand-grain weight (TGW), 30 for grain length (GL), three for grain width (GW), five for spike length (SL) and nine for stress tolerance index (STI) QTL in wheat. These QTL, containing 72 single nucleotide polymorphisms (SNPs), explained 2.23 - 7.35% of the phenotypic variation across multiple environments. Eight stable SNPs on chromosomes 2A, 2D, 3B, 4A, 5B, 5D, and 7D were associated with phenotypic stability under NC and DT conditions. Two of these stable SNPs had association with TGW and STI. Several novel QTL for TGW, GL and SL were identified on different chromosomes. Three linked SNPs were transformed into kompetitive allele-specific PCR (KASP) markers. These results will facilitate the discovery of promising SNPs for yield-related traits and/or drought stress tolerance and will accelerate the development of new wheat varieties with desirable alleles.

Identification and validation of plant height, spike length and spike compactness loci in common wheat (Triticum aestivum L.)

BACKGROUND

Plant height (PH), spike length (SL) and spike compactness (SCN) are important agronomic traits in wheat due to their strong correlations with lodging and yield. Thus, dissection of their genetic basis is essential for the improvement of plant architecture and yield potential in wheat breeding. The objective of this study was to map quantitative trait loci (QTL) for PH, SL and SCN in a recombinant inbred line (RIL) population derived from the cross 'PuBing3228 × Gao8901' (PG-RIL) and to evaluate the potential values of these QTL to improve yield.

RESULTS

In the current study, Five, six and ten stable QTL for PH, SL, and SCN, respectively, were identified in at least two individual environments. Five major QTL QPh.cas-5A.3, QPh.cas-6A, QSl.cas-6B.2, QScn.cas-2B.2 and QScn.cas-6B explained 5.58-25.68% of the phenotypic variation. Notably, two, three and three novel stable QTL for PH, SL and SCN were identified in this study, which could provide further insights into the genetic factors that shape PH and spike morphology in wheat. Conditional QTL analysis revealed that QTL for SCN were mainly affected by SL. Moreover, a Kompetitive Allele Specific PCR (KASP) marker tightly linked to stable major QTL QPh.cas-5A.3 was developed and verified using the PG-RIL population and a natural population.

CONCLUSIONS

Twenty-one stable QTL related to PH, SL, and SCN were identified. These stable QTL and the user-friendly marker KASP8750 will facilitate future studies involving positional cloning and marker-assisted selection in breeding.

Genome-wide association study reveals structural chromosome variations with phenotypic effects in wheat (Triticum aestivum L.)

Structural chromosome variations (SCVs) are large-scale genomic variations that can be detected by fluorescence in situ hybridization (FISH). SCVs have played important roles in the genome evolution of wheat (Triticum aestivum L.), but little is known about their genetic effects. In this study, a total of 543 wheat accessions from the Chinese wheat mini-core collection and the Shanxi Province wheat collection were used for chromosome analysis using oligonucleotide probe multiplex FISH. A total of 139 SCVs including translocations, pericentric inversions, presence/absence variations (PAVs), and copy number variations (CNVs) in heterochromatin were identified at 230 loci. The distribution frequency of SCVs varied between ecological regions and between landraces and modern cultivars. Structural analysis using SCVs as markers clearly divided the landraces and modern cultivars into different groups. There are very clear instances illustrating alien introgression and wide application of foreign germplasms improved the chromosome diversity of Chinese modern wheat cultivars. A genome-wide association study (GWAS) identified 29 SCVs associated with 12 phenotypic traits, and five (RT4AS•4AL-1DS/1DL•1DS-4AL, Mg2A-3, Mr3B-10, Mr7B-13, and Mr4A-7) of them were further validated using a doubled haploid population and advanced sib-lines, implying the potential value of these SCVs. Importantly, the number of favored SCVs that were associated with agronomic trait improvement was significantly higher in modern cultivars compared to landraces, indicating positive selection in wheat breeding. This study demonstrates the significant effects of SCVs during wheat breeding and provides an efficient method of mining favored SCVs in wheat and other crops.

Wheat traits and the associated loci conferring radiation use efficiency

Wheat (Triticum aestivum L.) radiation use efficiency (RUE) must be raised through crop breeding to further increase the yield potential, as the harvest index is now close to its theoretical limit. Field experiments including 209 wheat cultivars which have been widely cultivated in China since the 1940s were conducted in two growing seasons (2018-2019 and 2019-2020) to evaluate the variations of phenological, physiological, plant architectural, and yield-related traits and their contributions to RUE and to identify limiting factors for wheat yield potential. The average annual genetic gain in grain yield was 0.60% (or 45.32 kg ha^-1  year^-1 ; R²  = 0.44, P < 0.01), mainly attributed to the gain in RUE (r = 0.85, P < 0.01). The net photosynthetic rates were positively and closely correlated with grain RUE and grain yield, suggesting source as a limiting factor to future yield gains. Thirty-four cultivars were identified, exhibiting not only high RUE, but also traits contributing to high RUE and 11 other critical traits - of known genetic basis - as potential parents for breeding to improve yield and RUE. Our findings reveal wheat traits and the associated loci conferring RUE, which are valuable for facilitating marker-assisted breeding to improve wheat RUE and yield potential.

Fine mapping of the reduced height gene Rht22 in tetraploid wheat landrace Jianyangailanmai (Triticum turgidum L.)

Rht22 was fine mapped in the interval of 0.53-1.48 Mb on 7AS, which reduces cell number of internode to cause semi-dwarfism in Jianyangailanmai. As a valuable germplasm resource for wheat genetic improvement, tetraploid wheat has several reduced height (Rht) and enhanced harvest index genes. Rht22, discovered in Jianyangailanmai (JAM, Triticum turgidum L., 2n = 4x = 28, AABB), significantly increases the spikelet number per spike, but its accurate chromosomal position is still unknown. In this study, a high-density genetic map was constructed using specific-length amplified fragment sequencing in an F₇ RIL_DJ population, which was derived from a cross between dwarf Polish wheat (T. polonicum L., 2n = 4x = 28, AABB) and JAM. Two plant height loci, Qph.sicau-4B and Qph.sicau-7A, were mapped on chromosomes 4BS and 7AS, respectively. Qph.sicau-7A was mapped to the 0.33-4.46 Mb interval on 7AS and likely represents the candidate region of Rht22. Fine mapping confirmed and narrowed Rht22 on chromosome arm 7AS between Xbag295.s53 and Xb295.191 in three different populations. The physical region ranged from 0.53 to 1.48 Mb and included 18 candidate genes. Transcriptome analysis of two pairs of near-isogenic lines revealed that 135 differentially expressed genes (DEGs) were associated with semi-dwarfism. Of these, the expression of 83 annotated DEGs involved in hormones synthesis and signal transduction, cell wall composition, DNA replication, microtubule and phragmoplast arrays was significantly down-regulated in the semi-dwarf line. Therefore, Rht22 causes semi-dwarfism in JAM by disrupting these cellular processes, which impairs cell proliferation and reduces internode cell number.

InDels Identification and Association Analysis with Spike and Awn Length in Chinese Wheat Mini-Core Collection

Diversity surveys of germplasm are important for gaining insight into the genomic basis for crop improvement; especially InDels, which are poorly understood in hexaploid common wheat. Here, we describe a map of 89,923 InDels from exome sequencing of 262 accessions of a Chinese wheat mini-core collection. Population structure analysis, principal component analysis and selective sweep analysis between landraces and cultivars were performed. Further genome-wide association study (GWAS) identified five QTL (Quantitative Trait Loci) that were associated with spike length, two of them, on chromosomes 2B and 6A, were detected in 10 phenotypic data sets. Assisted with RNA-seq data, we identified 14 and 21 genes, respectively that expressed in spike and rachis within the two QTL regions that can be further investigated for candidate genes discovery. Moreover, InDels were found to be associated with awn length on chromosomes 5A, 6B and 4A, which overlapped with previously reported genetic loci B1 (Tipped 1), B2 (Tipped 2) and Hd (Hooded). One of the genes TaAGL6 that was previously shown to affect floral organ development was found at the B2 locus to affect awn length development. Our study shows that trait-associated InDels may contribute to wheat improvement and may be valuable molecular markers for future wheat breeding.

Did Wheat Breeding Simultaneously Alter Grain Concentrations of Macro- and Micro-Nutrient Over the Past 80 Years of Cultivar Releasing in China?

Biofortification of wheat with mineral through crop breeding is a sustainable and cost-effective approach to address human mineral malnutrition. A better understanding of the trends of grain concentrations of mineral nutrients in wheat over the breeding period may help to assess the breeding progress to date. A 2-year field experiment using 138 Chinese wheat landraces and 154 cultivars was conducted. Grain concentrations of micronutrients (Cu and Mn) and macronutrients (N, P, and K) were measured and corrected for a yield level to elucidate the trends of these mineral nutrients over the 80 years of cultivar releasing and identify genetic variation for these mineral nutrients in cultivars and landraces. Large genetic variation exists for grain mineral nutrients concentrations among tested genotypes, indicating that selection for enhancing mineral nutrient concentrations in wheat is possible. Landraces showed a slightly wide genetic variation of grain Cu concentration and a much narrow variation of Mn concentration when compared to modern cultivars. Grain concentrations of Cu and Mn decreased slightly with increasing grain yield with a weak correlation, while N, P, and K concentrations declined obviously with increasing yield with a strong correlation, revealing that increased grain yield had a strong negative effect on grain concentration of macronutrients, but a relative weak negative effect on micronutrients concentrations. When considering the impact of the variation in yield on mineral concentrations, grain concentrations of Cu, Mn, N, P, and K in wheat cultivars released from 1933 to 2017 exhibited different trends with a year of variety release. Grain Cu, N, and P concentrations showed significant decreasing trends over a breeding period, while grain Mn and K concentrations showed no clear trend, suggesting wheat breeding in China over the past 80 years has decreased grain concentrations of Cu, N, and P, and did not alter Mn and K concentrations. Finally, a total of 14 outstanding accessions with high grain mineral nutrients concentrations/contents were identified, and these genotypes can be considered as promising donors for developing mineral-dense wheat cultivars.

Mining of Wheat Pm2 Alleles for Goal-Oriented Marker-Assisted Breeding

Powdery mildew of wheat, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating disease that seriously reduces yield and quality worldwide. Utilization of plant resistance genes is an attractive and effective strategy for controlling this disease. Among the reported powdery mildew (Pm) resistance genes, Pm2 exhibits a diverse resistance spectrum among its multiple alleles. It has been widely used in China for resistance breeding for powdery mildew. To mine more Pm2 alleles and clarify their distribution, we screened 33 wheat cultivars/breeding lines carrying Pm2 alleles from 641 wheat genotypes using diagnostic and Pm2-linked markers. To further investigate the relationships within the Pm2 alleles, we compared their resistance spectra, polymorphism of marker alleles and gene sequences, and found that they have identical marker alleles and gene sequences but diverse resistance spectra. In addition, the diagnostic kompetitive allele-specific PCR (KASP) marker, YTU-KASP-Pm2, was developed and was shown to detect all the Pm2 alleles in the different genetic backgrounds. These findings provide valuable information for the distribution and rational use of Pm2 alleles, push forward their marker-assisted breeding (MAS), and hence improve the control of wheat powdery mildew.