Homologous haplotypes, expression, genetic effects and geographic distribution of the wheat yield gene TaGW2

Independent genetic factors control floret number and spikelet number in Triticum turgidum ssp

Wheat grain yield is a complex trait resulting from a trade-off among many distinct components. During wheat evolution, domestication events and then modern breeding have strongly increased the yield potential of wheat plants, by enhancing spike fertility. To address the genetic bases of spike fertility in terms of spikelet number per spike and floret number per spikelet, a population of 110 recombinant inbred lines (RILS) obtained crossing a Triticum turgidum ssp. durum cultivar (Latino) and a T. dicoccum accession (MG5323) was exploited. Being a modern durum and a semi-domesticated genotype, respectively, the two parents differ for spike architecture and fertility, and thus the corresponding RIL population is the ideal genetic material to dissect genetic bases of yield components. The RIL population was phenotyped in four environments. Using a high-density SNP genetic map and taking advantage of several genome sequencing available for Triticeae, a total of 94 QTLs were identified for the eight traits considered; these QTLs were further reduced to 17 groups, based on their genetic and physical co-location. QTLs controlling floret number per spikelet and spikelet number per spike mapped in non-overlapping chromosomal regions, suggesting that independent genetic factors determine these fertility-related traits. The physical intervals of QTL groups were considered for possible co-location with known genes functionally involved in spike fertility traits and with yield-related QTLs previously mapped in tetraploid wheat. The most interesting result concerns a QTL group on chromosome 5B, associated with spikelet number per spike, since it could host genes still uncharacterized for their association to spike fertility. Finally, we identified two different regions where the trade-off between fertility related traits and kernel weight is overcome. Further analyses of these regions could pave the way for a future identification of new genetic loci contributing to fertility traits essential for yield improvement in durum wheat.

Fine mapping of a major QTL, qKl-1BL controlling kernel length in common wheat

KEY MESSAGE

A major stable QTL, qKl-1BL, for kernel length of wheat was narrowed down to a 2.04-Mb interval on chromosome 1BL; the candidate genes were predicated and the genetic effects on yield-related traits were characterized. As a key factor influencing kernel weight, wheat kernel shape is closely related to yield formation, and in turn affects both wheat processing quality and market value. Fine mapping of the major quantitative trait loci (QTL) for kernel shape could provide genetic resources and a theoretical basis for the genetic improvement of wheat yield-related traits. In this study, a major QTL for kernel length (KL) on 1BL, named qKl-1BL, was identified from the recombinant inbred lines (RIL) in multiple environments based on the genetic map and physical map, with 4.76-21.15% of the phenotypic variation explained. To fine map qKl-1BL, the map-based cloning strategy was used. By using developed InDel markers, the near-isogenic line (NIL) pairs and eight key recombinants were identified from a segregating population containing 3621 individuals derived from residual heterozygous lines (RHLs) self-crossing. In combination with phenotype identification, qKl-1BL was finely positioned into a 2.04-Mb interval, KN1B:698.15-700.19 Mb, with eight differentially expressed genes enriched at the key period of kernel elongation. Based on transcriptome analysis and functional annotation information, two candidate genes for qKl-1BL controlling kernel elongation were identified. Additionally, genetic effect analysis showed that the superior allele of qKl-1BL from Jing411 could increase KL, thousand kernel weight (TKW), and yield per plant (YPP) significantly, as well as kernel bulk density and stability time. Taken together, this study identified a QTL interval for controlling kernel length with two possible candidate genes, which provides an important basis for qKl-1BL cloning, functional analysis, and application in molecular breeding programs.

A novel variation of TaGW2-6B increases grain weight without penalty in grain protein content in wheat (Triticum aestivum L.)

Yield and quality are two crucial breeding objects of wheat therein grain weight and grain protein content (GPC) are two key relevant factors correspondingly. Investigations of their genetic mechanisms represent special significance for breeding. In this study, 199 F2 plants and corresponding F2:3 families derived from Nongda3753 (ND3753) and its EMS-generated mutant 564 (M564) were used to investigate the genetic basis of larger grain and higher GPC of M564. QTL analysis identified a total of 33 environmentally stable QTLs related to thousand grain weight (TGW), grain area (GA), grain circle (GC), grain length (GL), grain width (GW), and GPC on chromosomes 1B, 2A, 2B, 4D, 6B, and 7D, respectively, among which QGw.cau-6B.1, QTgw.cau-6B.1, QGa.cau-6B.1, and QGc.cau-6B.1 shared overlap confidence interval on chromosome 6B. This interval contained the TaGW2 gene playing the same role as the QTLs, so TaGW2-6B was cloned and sequenced. Sequence alignment revealed two G/A SNPs between two parents, among which the SNP in the seventh exon led to a premature termination in M564. A KASP marker was developed based on the SNP, and single-marker analysis on biparental populations showed that the mutant allele could significantly increase GW and TGW, but had no effect on GPC. Distribution detection of the mutant allele through KASP marker genotyping and sequence alignment against databases ascertained that no materials harbored this allele within natural populations. This allele was subsequently introduced into three different varieties through molecular marker-assisted backcrossing, and it was revealed that the allele had a significant effect on simultaneously increasing GW, TGW, and even GPC in all of three backgrounds. Summing up the above, it could be concluded that a novel elite allele of TaGW2-6B was artificially created and might play an important role in wheat breeding for high yield and quality.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01455-y.

Breeding effects on durum wheat traits detected using GWAS and haplotype block analysis

Introduction

The recent boosting of genomic data in durum wheat (Triticum turgidum subsp. durum) offers the opportunity to better understand the effects of breeding on the genetic structures that regulate the expression of traits of agronomic interest. Furthermore, the identification of DNA markers useful for marker-assisted selection could also improve the reliability of technical protocols used for variety protection and registration.

Methods

Within this motivation context, 123 durum wheat accessions, classified into three groups: landraces (LR), ancient (OC) and modern cultivars (MC), were evaluated in two locations, for 34 agronomic traits, including UPOV descriptors, to assess the impact of changes that occurred during modern breeding.

Results

The association mapping analysis, performed with 4,241 SNP markers and six multi-locus-GWAS models, revealed 28 reliable Quantitative Trait Nucleotides (QTNs) related to plant morphology and kernel-related traits. Some important genes controlling flowering time and plant height were in linkage disequilibrium (LD) decay with QTNs identified in this study. A strong association for yellow berry was found on chromosome 6A (Q.Yb-6A) in a region containing the nadh-ubiquinone oxidoreductase subunit, a gene involved in starch metabolism. The Q.Kcp-2A harbored the PPO locus, with the associated marker (Ku_c13700_1196) in LD decay with Ppo-A1 and Ppo-A2. Interestingly, the Q.FGSGls-2B.1, identified by RAC875_c34512_685 for flag leaf glaucosity, mapped less than 1 Mb from the Epistatic inhibitors of glaucousness (Iw1), thus representing a good candidate for supporting the morphological DUS traits also with molecular markers. LD haplotype block approach revealed a higher diversity, richness and length of haploblocks in MC than OC and LR (580 in LR, 585 in OC and 612 in MC), suggesting a possible effect exerted by breeding programs on genomic regions associated with the agronomic traits.

Discussion

Our findings pave new ways to support the phenotypic characterization necessary for variety registration by using a panel of cost-effectiveness SNP markers associated also to the UPOV descriptors. Moreover, the panel of associated SNPs might represent a reservoir of favourable alleles to use in durum wheat breeding and genetics.

A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat

BACKGROUND

Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments.

RESULTS

We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection.

CONCLUSION

Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.

Genomics for Yield and Yield Components in Durum Wheat

In recent years, many efforts have been conducted to dissect the genetic basis of yield and yield components in durum wheat thanks to linkage mapping and genome-wide association studies. In this review, starting from the analysis of the genetic bases that regulate the expression of yield for developing new durum wheat varieties, we have highlighted how, currently, the reductionist approach, i.e., dissecting the yield into its individual components, does not seem capable of ensuring significant yield increases due to diminishing resources, land loss, and ongoing climate change. However, despite the identification of genes and/or chromosomal regions, controlling the grain yield in durum wheat is still a challenge, mainly due to the polyploidy level of this species. In the review, we underline that the next-generation sequencing (NGS) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms, as well as genome editing technology, will revolutionize plant breeding by providing a great opportunity to capture genetic variation that can be used in breeding programs. To date, genomic selection provides a valuable tool for modeling optimal allelic combinations across the whole genome that maximize the phenotypic potential of an individual under a given environment.

Responses of wheat kernel weight to diverse allelic combinations under projected climate change conditions

INTRODUCTION

In wheat, kernel weight (KW) is a key determinant of grain yield (GY). However, it is often overlooked when improving wheat productivity under climate warming. Moreover, little is known about the complex effects of genetic and climatic factors on KW. Here, we explored the responses of wheat KW to diverse allelic combinations under projected climate warming conditions.

METHODS

To focus on KW, we selected a subset of 81 out of 209 wheat varieties with similar GY, biomass, and kernel number (KN) and focused on their thousand-kernel weight (TKW). We genotyped them at eight kompetitive allele-specific polymerase chain reaction markers closely associated with TKW. Subsequently, we calibrated and evaluated the process-based model known as Agricultural Production Systems Simulator (APSIM-Wheat) based on a unique dataset including phenotyping, genotyping, climate, soil physicochemistry, and on-farm management information. We then used the calibrated APSIM-Wheat model to estimate TKW under eight allelic combinations (81 wheat varieties), seven sowing dates, and the shared socioeconomic pathways (SSPs) designated SSP2-4.5 and SSP5-8.5, driven by climate projections from five General Circulation Models (GCMs) BCC-CSM2-MR, CanESM5, EC-Earth3-Veg, MIROC-ES2L, and UKESM1-0-LL.

RESULTS

The APSIM-Wheat model reliably simulated wheat TKW with a root mean square error (RMSE) of < 3.076 g TK^-1 and R² of > 0.575 (P < 0.001). The analysis of variance based on the simulation output showed that allelic combination, climate scenario, and sowing date extremely significantly affected TKW (P < 0.001). The impact of the interaction allelic combination × climate scenario on TKW was also significant (P < 0.05). Meanwhile, the variety parameters and their relative importance in the APSIM-Wheat model accorded with the expression of the allelic combinations. Under the projected climate scenarios, the favorable allelic combinations (TaCKX-D1b + Hap-7A-1 + Hap-T + Hap-6A-G + Hap-6B-1 + H1g + A1b for SSP2-4.5 and SSP5-8.5) mitigated the negative effects of climate change on TKW.

DISCUSSION

The present study demonstrated that optimizing favorable allelic combinations can help achieve high wheat TKW. The findings of this study clarify the responses of wheat KW to diverse allelic combinations under projected climate change conditions. Additionally, the present study provides theoretical and practical reference for marker-assisted selection of high TKW in wheat breeding.

TaSPL14-7A is a conserved regulator controlling plant architecture and yield traits in common wheat (Triticum aestivum L.)

Plant architecture is a crucial influencing factor of wheat yield and adaptation. In this study, we cloned and characterized TaSPL14, a homologous gene of the rice ideal plant architecture gene OsSPL14 in wheat. TaSPL14 homoeologs (TaSPL14-7A, TaSPL14-7B and TaSPL14-7D) exhibited similar expression patterns, and they were all preferentially expressed in stems at the elongation stage and in young spikes. Moreover, the expression level of TaSPL14-7A was higher than that of TaSPL14-7B and TaSPL14-7D. Overexpression of TaSPL14-7A in wheat resulted in significant changes in plant architecture and yield traits, including decreased tiller number and increased kernel size and weight. Three TaSPL14-7A haplotypes were identified in Chinese wheat core collection, and haplotype-based association analysis showed that TaSPL14-7A-Hap1/2 were significantly correlated with fewer tillers, larger kernels and higher kernel weights in modern cultivars. The haplotype effect resulted from a difference in TaSPL14-7A expression levels among genotypes, with TaSPL14-7A-Hap1/2 leading to higher expression levels than TaSPL14-7A-Hap3. As favorable haplotypes, TaSPL14-7A-Hap1/2 underwent positive selection during global wheat breeding over the last century. Together, the findings of our study provide insight into the function and genetic effects of TaSPL14 and provide a useful molecular marker for wheat breeding.

Genome-Wide Association Study in Bread Wheat Identifies Genomic Regions Associated with Grain Yield and Quality under Contrasting Water Availability

The objectives of this study were to identify genetic loci in the bread wheat genome that would influence yield stability and quality under water stress, and to identify accessions that can be recommended for cultivation in dry and hot regions. We performed a genome-wide association study (GWAS) using a panel of 232 wheat accessions spanning diverse ecogeographic regions. Plants were evaluated in the Israeli Northern Negev, under two environments: water-limited (D; 250 mm) and well-watered (W; 450 mm) conditions; they were genotyped with ~71,500 SNPs derived from exome capture sequencing. Of the 14 phenotypic traits evaluated, 12 had significantly lower values under D compared to W conditions, while the values for two traits were higher under D. High heritability (H2 = 0.5-0.9) was observed for grain yield, spike weight, number of grains per spike, peduncle length, and plant height. Days to heading and grain yield could be partitioned based on accession origins. GWAS identified 154 marker-trait associations (MTAs) for yield and quality-related traits, 82 under D and 72 under W, and identified potential candidate genes. We identified 24 accessions showing high and/or stable yields under D conditions that can be recommended for cultivation in regions under the threat of global climate change.

The brassinosteroid biosynthesis gene TaD11-2A controls grain size and its elite haplotype improves wheat grain yields

TaD11-2A affects grain size and root length and its natural variations are associated with significant differences in yield-related traits in wheat. Brassinosteroids (BRs) control many important agronomic traits and therefore the manipulation of BR components could improve crop productivity and performance. However, the potential effects of BR-related genes on yield-related traits and stress tolerance in wheat (Triticum aestivum L.) remain poorly understood. Here, we identified TaD11 genes in wheat (rice D11 orthologs) that encoded enzymes involved in BR biosynthesis. TaD11 genes were highly expressed in roots (Zadoks scale: Z11) and grains (Z75), while expression was significantly suppressed by exogenous BR (24-epiBL). Ectopic expression of TaD11-2A rescued the abnormal panicle structure and plant height (PH) of the clustered primary branch 1 (cpb1) mutant, and also increased endogenous BR levels, resulting in improved grain yields and grain quality in rice. The tad11-2a-1 mutant displayed dwarfism, smaller grains, sensitivity to 24-epiBL, and reduced endogenous BR contents. Natural variations in TaD11-2A were associated with significant differences in yield-related traits, including PH, grain width, 1000-grain weight, and grain yield per plant, and its favorable haplotype, TaD11-2A-HapI was subjected to positive selection during wheat breeding. Additionally, TaD11-2A influenced root length and salt tolerance in rice and wheat at seedling stages. These results indicated the important role of BR TaD11 biosynthetic genes in controlling grain size and root length, and also highlighted their potential in the molecular biological analysis of wheat.

Exploiting Wild Emmer Wheat Diversity to Improve Wheat A and B Genomes in Breeding for Heat Stress Adaptation

Wheat is highly sensitive to temperature beyond the optimum. To improve wheat adaptation to heat stress, the best option is to exploit the diversity of wild wheat progenitors. This study aimed to identify germplasm and quantitative trait loci associated with heat stress tolerance from wild emmer wheat diversity. We evaluated a diverse set of multiple derivative lines harboring chromosome segments from nine wild emmer wheat parents under four environments: two optimum environments at Tottori, Japan and Dongola, Sudan, one moderate heat stress environment, and one severe heat stress environment at Wad Medani, Sudan. Genome-wide association analysis was conducted with 13,312 SNP markers. Strong marker-trait associations (MTAs) were identified for chlorophyll content at maturity on chromosomes 1A and 5B: these MTAs explained 28.8 and 26.8% of the variation, respectively. A region on chromosome 3A (473.7-638.4 Mbp) contained MTAs controlling grain yield, under optimum and severe heat stress. Under severe heat stress, regions on chromosomes 3A (590.4-713.3 Mbp) controlled grain yield, biomass, days to maturity and thousand kernel weight, and on 3B (744.0-795.2 Mbp) grain yield and biomass. Heat tolerance efficiency (HTE) was controlled by three MTAs, one each on chromosomes 2A, 2B, and 5A under moderate heat stress and one MTA on chromosome 3A under severe heat stress. Some of the MTAs found here were previously reported, but the new ones originated from the wild emmer wheat genomes. The favorable alleles identified from wild emmer wheat were absent or rare in the elite durum wheat germplasm being bred for heat stress tolerance. This study provides potential genetic materials, alleles, MTAs, and quantitative trait loci for enhancing wheat adaptation to heat stress. The derivative lines studied here could be investigated to enhance other stress tolerance such as drought and salinity.

A superior allele of the wheat gene TaGL3.3-5B, selected in the breeding process, contributes to seed size and weight

A superior allele of wheat gene TaGL3.3-5B was identified and could be used in marker-assisted breeding in wheat. Identifying the main genes which mainly regulate the yield-associated traits can significantly increase the wheat production. In this study, gene TaGL3.3 was cloned from common wheat according to the sequence of OsPPKL3. A SNP in the 8th exon of TaGL3.3-5B, T/C in coding sequence (CDS), which resulted in an amino acid change (Val/Ala), was identified between the low 1000-kernel weight (TKW) wheat Chinese Spring and the high TKW wheat Xinong 817 (817). Subsequently, association analysis in the mini-core collection (MCC) and the recombinant inbred lines (RIL) revealed that the allele TaGL3.3-5B-C (from 817) was significantly correlated with higher TKW. The high frequency of TaGL3.3-5B-C in the Chinese modern wheat cultivars indicated that it was selected positively in wheat breeding programs. The overexpression of TaGL3.3-5B-C in Arabidopsis resulted in shorter pods and longer grains than those of wild-type counterparts. Additionally, TaGL3.3 expressed a tissue-specific pattern in wheat as revealed by qRT-PCR. We also found that 817 showed higher expression of TaGL3.3 than that in Chinese Spring (CS) during the seed development. These results demonstrate that TaGL3.3 plays an important role in the formation of seed size and weight. Allele TaGL3.3-5B-C is associated with larger and heavier grains that are beneficial to wheat yield improvement.

Characterization of TaSPP-5A gene associated with sucrose content in wheat (Triticum aestivum L.)

BACKGROUND

Sucrose, the major product of photosynthesis and the primary sugar transported as a soluble carbohydrate via the phloem, is a critical determinant for harvest yield in wheat crops. Sucrose-phosphatase (SPP) catalyzes the final step in the sucrose biosynthesis pathway, implying its essential role in the plant.

RESULT

In this study, wheat SPP homologs genes were isolated from chromosomes 5A, 5B, and 5D, designated as TaSPP-5A, TaSPP-5B, and TaSPP-5D, respectively. Sequence alignment showed one 1-bp Insertion-deletion (InDel) and three single nucleotide polymorphisms (SNPs) at TaSPP-5A coding region, forming two haplotypes, TaSPP-5Aa and TaSPP-5Ab, respectively. A derived cleaved amplified polymorphism sequence (dCAPS) marker, TaSPP-5A-dCAPS, was developed to discriminate allelic variation based on the polymorphism at position 1242 (C-T). A total of 158 varieties were used to perform a TaSPP-5A marker-trait association analysis, where two haplotypes were significantly associated with sucrose content in two environments and with thousand-grain weight (TGW) and grain length (GL) in three environments. Quantitative real-time PCR further revealed that TaSPP-5Aa showed relatively higher expression than TaSPP-5Ab in wheat seedling leaves, generally associating with increased sucrose content and TGW. The expression of TaSPP-5A and sucrose content in TaSPP-5Aa haplotypes were also higher than those in TaSPP-5Ab haplotypes under both 20% PEG-6000 and 100 μM ABA treatment. Sequence alignment showed that the two TaSPP-5A haplotypes comprised 11 SNPs from -395 to -1962 bp at TaSPP-5A promoter locus, participating in the formation of several conserved sequences, may account for the high expression of TaSPP-5A in TaSPP-5Aa haplotypes. In addition, the distribution analysis of TaSPP-5A haplotypes revealed that TaSPP-5Aa was preferred in the natural wheat population, being strongly positively selected in breeding programs.

CONCLUSION

According to the SNPs detected in the TaSPP-5A sequence, two haplotypes, TaSPP-5Aa and TaSPP-5Ab, were identified among wheat accessions, which potential value for sucrose content selection was validated by association analysis. Our results indicate that the favorable allelic variation TaSPP-5Aa should be valuable in enhancing grain yield by improving the sucrose content. Furthermore, a functional marker, TaSPP-5A-dCAPS, can be used for marker-assisted selection to improve grain weight in wheat and provides insights into the biological function of TaSPP-5A gene.

CRISPR-Cas9 mediated mutation in GRAIN WIDTH and WEIGHT2 (GW2) locus improves aleurone layer and grain nutritional quality in rice

Enhancing crop productivity and their nutritional quality are the key components and primary focus of crop improvement strategy for fulfilling future food demand and improving human health. Grain filling and endosperm development are the key determinants of grain yield and nutritional quality. GRAIN WIDTH and WEIGHT2 (GW2) gene encodes a RING-type E3 ubiquitin ligase and determines the grain weight in cereal crops. Here we report GW2 knockout (KO) mutants in Indica (var. MTU1010) through CRISPR/Cas9 genome editing. The endosperm of GW2-KO mutant seed displays a thick aleurone layer with enhanced grain protein content. Further the loss of function of OsGW2 results in improved accumulation of essential dietary minerals (Fe, Zn, K, P, Ca) in the endosperm of rice grain. Additionally, the mutants displayed an early growth vigour phenotype with an improved root and shoot architecture. The hull morphology of GW2-KO lines also showed improved, grain filling thereby promoting larger grain architecture. Together, our findings indicate that GW2 may serve as a key regulator of improved grain architecture, grain nutritional quality and an important modulator of plant morphology. The study offers a strategy for the development of improved rice cultivars with enriched nutritional quality and its possible implementation in other cereals as well.

Identification and fine mapping of alien fragments associated with enhanced grain weight from Agropyron cristatum chromosome 7P in common wheat backgrounds

An enhanced grain weight locus from Agropyron cristatum chromosome 7P was verified in two wheat backgrounds, localized to the 7PS1-2 region. Novel translocation lines with this locus were evaluated. Agropyron cristatum is a wild relative of wheat that harbours elite genes for wheat improvement. The wheat-A. cristatum 7P disomic addition line II-5-1 exhibits high grain weight. Here, to dissect the genetic basis of grain weight contributed by A. cristatum chromosome 7P in wheat backgrounds, four segregated populations of the addition line were developed and evaluated in two wheat backgrounds. The results showed that A. cristatum chromosome 7P can stably and significantly increase the grain weight by approximately 2 g, mainly by increasing grain length at different grain weight levels of the wheat background. The locus for increased grain weight from chromosome 7P shows dominant inheritance independent of the wheat background. Moreover, two deletion lines and 23 translocation lines were identified by cytological methods and molecular markers, and an enlarged chromosome 7P bin map was constructed with 158 STS markers and 40 bin intervals. With the genetic populations of these deletion and translocation lines, the genetic locus of increased grain weight was narrowed down to bin 7PS1-2. Two translocation lines (7PT-A18 and 7PT-B4) with smaller 7P chromosomal segments exhibited an increase in grain weight, grain length and grain width simultaneously. These translocation lines carrying the 7PS1-2 chromosomal fragment will be valuable genetic resources for wheat grain weight improvement. Collectively, this study uncovers the grain weight locus from chromosome 7P and provides novel pre-breeding lines with enhanced grain weight.

Direct introgression of untapped diversity into elite wheat lines

The effective utilization of natural variation has become essential in addressing the challenges that climate change and population growth pose to global food security. Currently adopted protracted approaches to introgress exotic alleles into elite cultivars need substantial transformation. Here, through a strategic three-way crossing scheme among diverse exotics and the best historical elites (exotic/elite1//elite2), 2,867 pre-breeding lines were developed, genotyped and screened for multiple agronomic traits in four mega-environments. A meta-genome-wide association study, selective sweeps and haplotype-block-based analyses unveiled selection footprints in the genomes of pre-breeding lines as well as exotic-specific associations with agronomic traits. A simulation with a neutrality assumption demonstrated that many pre-breeding lines had significant exotic contributions despite substantial selection bias towards elite genomes. National breeding programmes worldwide have adopted 95 lines for germplasm enhancement, and 7 additional lines are being advanced in varietal release trials. This study presents a great leap forwards in the mobilization of GenBank variation to the breeding pipelines.

Heterologous expression of ZmGS5 enhances organ size and seed weight by regulating cell expansion in Arabidopsis thaliana

Maize ZmGS5 was reported to be positively associated with kernel-related traits, however, its regulatory mechanism on plant development and seed size remains unknown. In this study, ZmGS5 was demonstrated to be widely expressed in various maize tissues with the highest expression level in developing embryos, indicating its critical roles in early kernel development process. The ZmGS5 protein was subcellularly localized to both the nucleus and cytoplasm. Transgenic Arabidopsis plants overexpressing ZmGS5 under the control of either the constitutive maize Ubiquitin1 promotor or native ZmGS5 promoter resulted in increased plant size, biomass, seed size and weight, although no significant difference was observed between transgenic lines harboring the two constructs. In contrast, the antisense-ZmGS5 transgene resulted in opposite phenotypes. Our cytological data suggested that ZmGS5 enlarged petal size through enhancing cell expansion. Quantitative RT-PCR analysis indicated that ZmGS5 might enhance cell expansion and grain filling by upregulating expression levels of particular EXPA or SWEET genes. Collectively, these findings help us further understand the biological function and regulatory mechanism of ZmGS5 in improving organ size and seed weight, which imply its great potential for high-yield breeding in the future.

The physiology and genetics behind fruiting efficiency: a promising spike trait to improve wheat yield potential

Fruiting efficiency (FE, grains per g of spike dry weight at anthesis) was proposed as a promising spike trait to improve wheat yield potential, based on its functional relationship with grain number determination and the evidence of trait variability in elite germplasm. During the last few years, we have witnessed great advances in the understanding of the physiological and genetic basis of this trait. The present review summarizes the recent heritability estimations and the genetic gains obtained when fruiting efficiency was measured at maturity (FEm, grains per g of chaff) and used as selection criterion. In addition, we propose spike ideotypes for contrasting fruiting efficiencies based on the fertile floret efficiency (FFE, fertile florets per g of spike dry weight at anthesis) and grain set (grains per fertile floret), together with other spike fertility-related traits. We also review novel genes and quantitative trait loci available for using marker-assisted selection for fruiting efficiency and other spike fertility traits. The possible trade-off between FE and grain weight and the genes reported to alter this relation are also considered. Finally, we discuss the benefits and future steps towards the use of fruiting efficiency as a selection criterion in breeding programs.

Combining Protein Content and Grain Yield by Genetic Dissection in Bread Wheat under Low-Input Management

The simultaneous improvement of protein content (PC) and grain yield (GY) in bread wheat (Triticum aestivum L.) under low-input management enables the development of resource-use efficient varieties that combine high grain yield potential with desirable end-use quality. However, the complex mechanisms of genotype, management, and growing season, and the negative correlation between PC and GY complicate the simultaneous improvement of PC and GY under low-input management. To identify favorable genotypes for PC and GY under low-input management, this study used 209 wheat varieties, including strong gluten, medium-strong gluten, medium gluten, weak gluten, winter, semi-winter, weak-spring, and spring types, which has been promoted from the 1980s to the 2010s. Allelic genotyping, performed using kompetitive allele-specific polymerase chain reaction (KASP) technology, found 69 types of GY-PC allelic combinations in the tested materials. Field trials were conducted with two growing season treatments (2018–2019 and 2019–2020) and two management treatments (conventional management and low-input management). Multi-environment analysis of variance showed that genotype, management, and growing season had extremely substantial effects on wheat GY and PC, respectively, and the interaction of management × growing season also had extremely significant effects on wheat GY. According to the three-sigma rule of the normal distribution, the GY of wheat varieties Liangxing 66 and Xinmai 18 were stable among the top 15.87% of all tested materials with high GY, and their PC reached mean levels under low-input management, but also stably expressed high GY and high PC under conventional management, which represents a great development potential. These varieties can be used as cultivars of interest for breeding because TaSus1-7A, TaSus1-7B, TaGW2-6A, and TaGW2-6B, which are related to GY, and Glu-B3, which is related to PC, carry favorable alleles, among which Hap-1/2, the allele of TaSus1-7A, and Glu-B3b/d/g/i, the allele of Glu-B3, can be stably expressed. Our results may be used to facilitate the development of high-yielding and high-quality wheat varieties under low-input management, which is critical for sustainable food and nutrition security.

Functional gene assessment of bread wheat: breeding implications in Ningxia Province

BACKGROUND

The overall genetic distribution and divergence of cloned genes among bread wheat varieties that have occurred during the breeding process over the past few decades in Ningxia Province, China, are poorly understood. Here, we report the genetic diversities of 44 important genes related to grain yield, quality, adaptation and resistance in 121 Ningxia and 86 introduced wheat cultivars and advanced lines.

RESULTS

The population structure indicated characteristics of genetic components of Ningxia wheat, including landraces of particular genetic resources, introduced varieties with rich genetic diversities and modern cultivars in different periods. Analysis of allele frequencies showed that the dwarfing alleles Rht-B1b at Rht-B1 and Rht-D1b at Rht-D1, 1BL/1RS translocation, Hap-1 at GW2-6B and Hap-H at Sus2-2B are very frequently present in modern Ningxia cultivars and in introduced varieties from other regions but absent in landraces. This indicates that the introduced wheat germplasm with numerous beneficial genes is vital for broadening the genetic diversity of Ningxia wheat varieties. Large population differentiation between modern cultivars and landraces has occurred in adaptation genes. Founder parents carry excellent allele combinations of important genes, with a higher number of favorable alleles than modern cultivars. Gene flow analysis showed that six founder parents have greatly contributed to breeding improvement in Ningxia Province, particularly Zhou 8425B, for yield-related genes.

CONCLUSIONS

Varieties introduced from other regions with rich genetic diversity and landraces with well-adapted genetic resources have been applied to improve modern cultivars. Founder parents, particularly Zhou 8425B, for yield-related genes have contributed greatly to wheat breeding improvement in Ningxia Province. These findings will greatly benefit bread wheat breeding in Ningxia Province as well as other areas with similar ecological environments.

Identification and validation of quantitative trait loci for kernel traits in common wheat (Triticum aestivum L.)

BACKGROUND

Kernel weight and morphology are important traits affecting cereal yields and quality. Dissecting the genetic basis of thousand kernel weight (TKW) and its related traits is an effective method to improve wheat yield.

RESULTS

In this study, we performed quantitative trait loci (QTL) analysis using recombinant inbred lines derived from the cross 'PuBing3228 × Gao8901' (PG-RIL) to dissect the genetic basis of kernel traits. A total of 17 stable QTLs related to kernel traits were identified, notably, two stable QTLs QTkw.cas-1A.2 and QTkw.cas-4A explained the largest portion of the phenotypic variance for TKW and kernel length (KL), and the other two stable QTLs QTkw.cas-6A.1 and QTkw.cas-7D.2 contributed more effects on kernel width (KW). Conditional QTL analysis revealed that the stable QTLs for TKW were mainly affected by KW. The QTLs QTkw.cas-7D.2 and QKw.cas-7D.1 associated with TKW and KW were delimited to the physical interval of approximately 3.82 Mb harboring 47 candidate genes. Among them, the candidate gene TaFT-D1 had a 1 bp insertions/deletion (InDel) within the third exon, which might be the reason for diversity in TKW and KW between the two parents. A Kompetitive Allele-Specific PCR (KASP) marker of TaFT-D1 allele was developed and verified by PG-RIL and a natural population consisted of 141 cultivar/lines. It was found that the favorable TaFT-D1 (G)-allele has been positively selected during Chinese wheat breeding. Thus, these results can be used for further positional cloning and marker-assisted selection in wheat breeding programs.

CONCLUSIONS

Seventeen stable QTLs related to kernel traits were identified. The stable QTLs for thousand kernel weight were mainly affected by kernel width. TaFT-D1 could be the candidate gene for QTLs QTkw.cas-7D.2 and QKw.cas-7D.1.

Identification and Validation of New Stable QTLs for Grain Weight and Size by Multiple Mapping Models in Common Wheat

Improvement of grain weight and size is an important objective for high-yield wheat breeding. In this study, 174 recombinant inbred lines (RILs) derived from the cross between Jing 411 and Hongmangchun 21 were used to construct a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq). Three mapping methods, including inclusive composite interval mapping (ICIM), genome-wide composite interval mapping (GCIM), and a mixed linear model performed with forward-backward stepwise (NWIM), were used to identify QTLs for thousand grain weight (TGW), grain width (GW), and grain length (GL). In total, we identified 30, 15, and 18 putative QTLs for TGW, GW, and GL that explain 1.1-33.9%, 3.1%-34.2%, and 1.7%-22.8% of the phenotypic variances, respectively. Among these, 19 (63.3%) QTLs for TGW, 10 (66.7%) for GW, and 7 (38.9%) for GL were consistent with those identified by genome-wide association analysis in 192 wheat varieties. Five new stable QTLs, including 3 for TGW (Qtgw.ahau-1B.1, Qtgw.ahau-4B.1, and Qtgw.ahau-4B.2) and 2 for GL (Qgl.ahau-2A.1 and Qgl.ahau-7A.2), were detected by the three aforementioned mapping methods across environments. Subsequently, five cleaved amplified polymorphic sequence (CAPS) markers corresponding to these QTLs were developed and validated in 180 Chinese mini-core wheat accessions. In addition, 19 potential candidate genes for Qtgw.ahau-4B.2 in a 0.31-Mb physical interval were further annotated, of which TraesCS4B02G376400 and TraesCS4B02G376800 encode a plasma membrane H+-ATPase and a serine/threonine-protein kinase, respectively. These new QTLs and CAPS markers will be useful for further marker-assisted selection and map-based cloning of target genes.

Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation

BACKGROUND

China has diverse wheat varieties that adapt to very different environments divided into ten agro-ecological zones. A better understanding of genomic differences and patterns of selection among agro-ecological zones could provide useful information in selection of specific adaptive traits in breeding.

RESULTS

We genotyped 438 wheat accessions from ten zones with kompetitive allele specific PCR (KASP) markers specific to 47 cloned genes for grain yield, quality, adaptation and stress resistance. Phylogenetic trees and principle component analysis revealed clear differences in winter and spring growth habits. Nucleotide diversity (π) and π ratio (π_CL/π_MCC) suggested that genetic diversity had increased during breeding, and that Chinese landraces (CL) from Zones I-V contributed little to modern Chinese cultivars (MCC). π ratio and Fst identified 24 KASP markers with 53 strong selection signals specific to Zones I (9 signals), II (12), III (5), IV (5), V (6), and VI (6). Genes with clear genetic differentiation and strong response to selection in at least three zones were leaf rust resistance gene Lr34 (I, II, III and IV), photoperiod sensitivity gene Ppd-D1 (I, II, III, IV and V), vernalization gene Vrn-B1 (V, VII, VIII and X), quality-related gene Glu-B1 (I, II and III) and yield-related genes Sus1-7B (I, II, III, IV and IX), Sus2-2A (I, II, III., IV and VI) and GW2-6B (II, V and VI).

CONCLUSIONS

This study examined selection of multiple genes in each zone, traced the distribution of important genetic variations and provided useful information for ecological genomics and enlightening future breeding goals for different agro-ecological zones.

Starch Metabolism in Wheat: Gene Variation and Association Analysis Reveal Additive Effects on Kernel Weight

Kernel weight is a key determinant of yield in wheat (Triticum aestivum L.). Starch consists of amylose and amylopectin and is the major constituent of mature grain. Therefore, starch metabolism in the endosperm during grain filling can influence kernel weight. In this study, we sequenced 87 genes involved in starch metabolism from 300 wheat accessions and detected 8,141 polymorphic sites. We also characterized yield-related traits across different years in these accessions. Although the starch contents fluctuated, thousand kernel weight (TKW) showed little variation. Polymorphisms in six genes were significantly associated with TKW. These genes were located on chromosomes 2A, 2B, 4A, and 7A; none were associated with starch content or amylose content. Variations of 15 genes on chromosomes 1A and 7A formed haplotype blocks in 26 accessions. Notably, accessions with higher TKWs had more of the favorable haplotypes. We thus conclude that these haplotypes contribute additive effects to TKW.

Molecular Mapping and Genomics of Grain Yield in Durum Wheat: A Review

Durum wheat is the most relevant cereal for the whole of Mediterranean agriculture, due to its intrinsic adaptation to dryland and semi-arid environments and to its strong historical cultivation tradition. It is not only relevant for the primary production sector, but also for the food industry chains associated with it. In Mediterranean environments, wheat is mostly grown under rainfed conditions and the crop is frequently exposed to environmental stresses, with high temperatures and water scarcity especially during the grain filling period. For these reasons, and due to recurrent disease epidemics, Mediterranean wheat productivity often remains under potential levels. Many studies, using both linkage analysis (LA) and a genome-wide association study (GWAS), have identified the genomic regions controlling the grain yield and the associated markers that can be used for marker-assisted selection (MAS) programs. Here, we have summarized all the current studies identifying quantitative trait loci (QTLs) and/or candidate genes involved in the main traits linked to grain yield: kernel weight, number of kernels per spike and number of spikes per unit area.

Characterization of glycerol-3-phosphate acyltransferase 9 (AhGPAT9) genes, their allelic polymorphism and association with oil content in peanut (Arachis hypogaea L.)

GPAT, the rate-limiting enzyme in triacylglycerol (TAG) synthesis, plays an important role in seed oil accumulation. In this study, two AhGPAT9 genes were individually cloned from the A- and B- genomes of peanut, which shared a similarity of 95.65%, with 165 site differences. The overexpression of AhGPAT9 or the knock-down of its gene expression increased or decreased the seed oil content, respectively. Allelic polymorphism analysis was conducted in 171 peanut germplasm, and 118 polymorphic sites in AhGPAT9A formed 64 haplotypes (a1 to a64), while 94 polymorphic sites in AhGPAT9B formed 75 haplotypes (b1 to b75). The haplotype analysis showed that a5, b57, b30 and b35 were elite haplotypes related to high oil content, whereas a7, a14, a48, b51 and b54 were low oil content types. Additionally, haplotype combinations a62/b10, a38/b31 and a43/b36 were associated with high oil content, but a9/b42 was a low oil content haplotype combination. The results will provide valuable clues for breeding new lines with higher seed oil content using hybrid polymerization of high-oil alleles of AhGPAT9A and AhGPAT9B genes.

Genetic architecture underpinning yield component traits in wheat

Genetic atlas, reliable QTL and candidate genes of yield component traits in wheat were figured out, laying concrete foundations for map-based gene cloning and dissection of regulatory mechanisms underlying yield. Mining genetic loci for yield is challenging due to the polygenic nature, large influence of environment and complex relationship among yield component traits (YCT). Many genetic loci related to wheat yield have been identified, but its genetic architecture and key genetic loci for selection are largely unknown. Wheat yield potential can be determined by three YCT, thousand kernel weight, kernel number per spike and spike number. Here, we summarized the genetic loci underpinning YCT from QTL mapping, association analysis and homology-based gene cloning. The major loci determining yield-associated agronomic traits, such as flowering time and plant height, were also included in comparative analyses with those for YCT. We integrated yield-related genetic loci onto chromosomes based on their physical locations. To identify the major stable loci for YCT, 58 QTL-rich clusters (QRC) were defined based on their distribution on chromosomes. Candidate genes in each QRC were predicted according to gene annotation of the wheat reference genome and previous information on validation of those genes in other species. Finally, a technological route was proposed to take full advantage of the resultant resources for gene cloning, molecular marker-assisted breeding and dissection of molecular regulatory mechanisms underlying wheat yield.

Genetics of yield, abiotic stress tolerance and biofortification in wheat (Triticum aestivum L.)

A review of the available literature on genetics of yield and its component traits, tolerance to abiotic stresses and biofortification should prove useful for future research in wheat in the genomics era. The work reviewed in this article mainly covers the available information on genetics of some important quantitative traits including yield and its components, tolerance to abiotic stresses (heat, drought, salinity and pre-harvest sprouting = PHS) and biofortification (Fe/Zn and phytate contents with HarvestPlus Program) in wheat. Major emphasis is laid on the recent literature on QTL interval mapping and genome-wide association studies, giving lists of known QTL and marker-trait associations. Candidate genes for different traits and the cloned and characterized genes for yield traits along with the molecular mechanism are also described. For each trait, an account of the present status of marker-assisted selection has also been included. The details of available results have largely been presented in the form of tables; some of these tables are included as supplementary files.

Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia

We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.

TaDA1, a conserved negative regulator of kernel size, has an additive effect with TaGW2 in common wheat (Triticum aestivum L.)

Kernel size is an important trait determining cereal yields. In this study, we cloned and characterized TaDA1, a conserved negative regulator of kernel size in wheat (Triticum aestivum). The overexpression of TaDA1 decreased the size and weight of wheat kernels, while its down-regulation using RNA interference (RNAi) had the opposite effect. Three TaDA1-A haplotypes were identified in Chinese wheat core collections, and a haplotype association analysis showed that TaDA1-A-HapI was significantly correlated with the production of larger kernels and higher kernel weights in modern Chinese cultivars. The haplotype effect resulted from a difference in TaDA1-A expression levels between genotypes, with TaDA1-A-HapI resulting in lower TaDA1-A expression levels. This favourable haplotype was found having been positively selected during wheat breeding over the last century. Furthermore, we demonstrated that TaDA1-A physically interacts with TaGW2-B. The additive effects of TaDA1-A and TaGW2-B on kernel weight were confirmed not only by the phenotypic enhancement arising from the simultaneous down-regulation of TaDA1 and TaGW2 expression, but also by the combinational haplotype effects estimated from multi-environment field data from 348 wheat cultivars. A comparative proteome analysis of developing transgenic and wild-type grains indicated that TaDA1 and TaGW2 are involved in partially overlapping but relatively independent protein regulatory networks. Thus, we have identified an important gene controlling kernel size in wheat and determined its interaction with other genes regulating kernel weight, which could have beneficial applications in wheat breeding.

SNP-based association study of kernel architecture in a worldwide collection of durum wheat germplasm

Durum wheat, genetic resource with favorable alleles is considered as natural gene pool for wheat breeding. Kernel size and weight are important factors affecting grain yield in crops. Here, association analysis was performed to dissect the genetic constitution of kernel-related traits in 150 lines collected from 46 countries and regions using a set of EST-derived and genome-wide SNP markers with five consecutive years of data. Total 109 significant associations for eight kernel-related traits were detected under a mix linear model, generating 54 unique SNP markers distributed on 13 of 14 chromosomes. Of which, 19 marker-trait associations were identified in two or more environments, including one stable and pleiotropic SNP BE500291_5_A_37 on chromosome 5A correlated with six kernel traits. Although most of our SNP loci were overlapped with the previously known kernel weight QTLs, several novel loci for kernel traits in durum were reported. Correlation analysis implied that the moderate climatic variables during growth and development of durum are needed for the large grain size and high grain weight. Combined with our previous studies, we found that chromosome 5A might play an important role in durum growth and development.

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.

Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding

Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued.

Molecular Characterization of 87 Functional Genes in Wheat Diversity Panel and Their Association With Phenotypes Under Well-Watered and Water-Limited Conditions

Modern breeding imposed selection for improved productivity that largely influenced the frequency of superior alleles underpinning traits of breeding interest. Therefore, molecular diagnosis for the allelic variations of such genes is important to manipulate beneficial alleles in wheat molecular breeding. We analyzed a diversity panel largely consisted of advanced lines derived from synthetic hexaploid wheats for allelic variation at 87 functional genes or loci of breeding importance using 124 high-throughput KASP markers. We also developed two KASP markers for water-soluble carbohydrate genes (TaSST-D1 and TaSST-A1) associated with plant height and thousand grain weight (TGW) in the diversity panel. KASP genotyping results indicated that beneficial alleles for genes underpinning flowering time (Ppd-D1 and Vrn-D3), thousand grain weight (TaCKX-D1, TaTGW6-A1, TaSus1-7B, and TaCwi-D1), water-soluble carbohydrates (TaSST-A1), yellow-pigment content (Psy-B1 and Zds-D1), and root lesion nematodes (Rlnn1) were fixed in diversity panel with frequency ranged from 96.4 to 100%. The association analysis of functional genes with agronomic and biochemical traits under well-watered (WW) and water-limited (WL) conditions revealed that 21 marker-trait associations (MTAs) were consistently detected in both moisture conditions. The major developmental genes such as Vrn-A1, Rht-D1, and Ppd-B1 had the confounding effect on several agronomic traits including plant height, grain size and weight, and grain yield in both WW and WL conditions. The accumulation of favorable alleles for grain size and weight genes additively enhanced grain weight in the diversity panel. Graphical genotyping approach was used to identify accessions with maximum number of favorable alleles, thus likely to have high breeding value. These results improved our knowledge on the selection of favorable and unfavorable alleles through unconscious selection breeding and identified the opportunities to deploy alleles with effects in wheat breeding.

Genome-wide haplotype analysis improves trait predictions in Brassica napus hybrids

Combining ability is crucial for parent selection in crop hybrid breeding. Many studies have attempted to provide reliable and quick methods to identify genome regions in parental lines correlating with improved hybrid performance. The local haplotype patterns surrounding densely spaced DNA markers include a large amount of genetic information, and analysis of the relationships between haplotypes and hybrid performance can provide insight into the underlying genome regions which might contribute to enhancing combining ability. Here, we generated 24,403 single-copy, genome-wide SNP loci and calculated the general combining ability (GCA) of 950 hybrids from a diverse panel of 475 pollinators of spring-type canola inbred lines crossed with two testers for days to flowering (DTF) and seed glucosinolate content (GSL). We performed a genome-wide analysis of the haplotypes and detected eight and seven haplotype regions that were significantly associated with the GCA values for DTF and seed GSL, respectively. Additionally, two haplotype blocks containing orthologs of flowering time genes FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC) on chromosome A02 showed additive epistatic interactions influencing flowering time. Moreover, two homoeologous haplotype regions on chromosomes A02 and C02 corresponded to major quantitative trait loci (QTL) for GSL which showed additive effects related to reduction of seed GSL in F1 hybrids. Our study showed that haplotype analysis has the potential to substantially improve the efficiency of hybrid breeding programs.

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

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.

Genomic Regions From an Iranian Landrace Increase Kernel Size in Durum Wheat

Kernel size and shape are important parameters determining the wheat profitability, being main determinants of yield and its technological quality. In this study, a segregating population of 118 recombinant inbred lines, derived from a cross between the Iranian durum landrace accession "Iran_249" and the Iranian durum cultivar "Zardak", was used to investigate durum wheat kernel morphology factors and their relationships with kernel weight, and to map the corresponding QTLs. A high density genetic map, based on wheat 90k iSelect Infinium SNP assay, comprising 6,195 markers, was developed and used to perform the QTL analysis for kernel length and width, traits related to kernel shape and weight, and heading date, using phenotypic data from three environments. Overall, a total of 31 different QTLs and 9 QTL interactions for kernel size, and 21 different QTLs and 5 QTL interactions for kernel shape were identified. The landrace Iran_249 contributed the allele with positive effect for most of the QTLs related to kernel length and kernel weight suggesting that the landrace might have considerable potential toward enhancing the existing gene pool for grain shape and size traits and for further yield improvement in wheat. The correlation among traits and co-localization of corresponding QTLs permitted to define 11 clusters suggesting causal relationships between simplest kernel size trait, like kernel length and width, and more complex secondary trait, like kernel shape and weight related traits. Lastly, the recent release of the T. durum reference genome sequence allowed to define the physical interval of our QTL/clusters and to hypothesize novel candidate genes inspecting the gene content of the genomic regions associated to target traits.

Distinguishing CPT gene family members and vetting the sequence structure of a putative rubber synthesizing variant in Hevea brasiliensis

cis-Prenyltransferases (cis-PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. cis-PTs catalyze the cis-1,4-polymerization of isoprene units to generate isoprenoids with carbon skeletons varying from C10 (neryl pyrophosphate) to C > 10,000 (natural rubber). Though the previously reported CPTs in Hevea are designated based on sequence variations, their classification was done mostly by phylogenetic analysis using a mixture of partial as well as full length sequences often excluding the UTRs. In this context an attempt was made to reclassify the CPTs strictly based on their sequence similarity and distinguish the members putatively associated with rubber biosynthesis from the others. Extensive computational analysis was carried out on CPT sequences obtained from public resources and whole genome assemblies of Hevea. Based on the results from BLAST analysis, multiple sequence alignments of protein, nucleotide and untranslated regions, open reading frame analysis, gene prediction analysis and sequence length variations, we conclude that there exists mainly three CPTs namely RubCPT1, RubCPT2 and RubCPT3 putatively associated with rubber biosynthesis in Hevea brasiliensis. The rest were categorised as variants of dehydrodolichyl diphosphate synthase (DHDDS) involved in the synthesis of dolichols having short chain isoprenoids. Analysis of the sequence structure of the most highly expressed RubCPT1 in latex revealed the allele richness and diversity of this important variant prevailing in the popular rubber clones. Haplotypes consisting of SNPs with high degree of heterozygosity were also identified. Segregation and linkage disequilibrium analysis confirmed that recombination is the major contributor towards the generation of allelic diversity rather than point mutations. Alternatively, gene expression analysis indicated the possibility of association between specific haplotypes and RubCPT1 expression in Hevea clones which may have downstream impact up to the level of rubber production. The conclusions from this study may pave way for the identification and better understanding of CPTs directly involved with natural rubber biosynthesis in Hevea and the SNP data generated may aid in the development of molecular markers putatively associated with yield in rubber.

TaBT1, affecting starch synthesis and thousand kernel weight, underwent strong selection during wheat improvement

BRITTLE1 (BT1), responsible for unidirectional transmembrane transport of ADP-glucose, plays a pivotal role in starch synthesis of cereal grain. In this study, we isolated three TaBT1 homoeologous genes located on chromosomes 6A, 6B, and 6D in common wheat. TaBT1 was mainly expressed in developing grains, and knockdown of TaBT1 in common wheat produced a decrease in grain size, thousand kernel weight (TKW), and grain total starch content. High diversity was detected at the TaBT1-6B locus, with 24 polymorphic sites forming three haplotypes (Hap1, Hap2, and Hap3). Association analysis revealed that Hap1 and Hap2 were preferred haplotypes in modern breeding, for their significant correlations with higher TKW. Furthermore, β-glucuronidase (GUS) staining and enzyme activity assays in developing grains of transgenic rice with exogenous promoters indicated that the promoters of Hap1 and Hap2 showed stronger driving activity than that of Hap3. Evolutionary analysis revealed that BT1 underwent strong selection during wheat polyploidization. In addition, the frequency distribution of TaBT1-6B haplotypes revealed that Hap1 and Hap2 were preferred in global modern wheat cultivars. Our findings suggest that TaBT1 has an important effect on starch synthesis and TKW, and provide two valuable molecular markers for marker assisted selection (MAS) in wheat high-yield breeding.

Genome-wide association study revealed that the TaGW8 gene was associated with kernel size in Chinese bread wheat

Using Wheat 90 K SNP assay, kernel-related traits of Chinese bread wheat were used to perform association mapping in 14 environments by GWAS. Results indicated that 996 and 953 of 4417 and 3172 significant SNPs for kernel length and thousand-kernel weight were located on the chromosome 7B. Haplotype analysis of these SNPs on 7B generated the block containing the predicted TaGW8-B1 gene. TaGW8-B1 gene was further cloned by sequencing in bread wheat and a 276-bp InDel was found in the first intron. TaGW8-B1 without and with the 276-bp InDel were designated as TaGW8-B1a and TaGW8-B1b, respectively. Analysis of agronomic traits indicated that cultivars with TaGW8-B1a possessed significantly wider kernel width, significantly more kernel number per spike, longer kernel length, higher thousand-kernel weight and more spikelet number per spike than cultivars with TaGW8-B1b. Furthermore, cultivars with TaGW8-B1a possessed significantly higher yield than cultivars with TaGW8-B1b. Therefore, TaGW8-B1a was considered as a potentially superior allele. Meanwhile, TaGW8-B1a possessed a significantly higher expression level than TaGW8-B1b in mature seeds by qRT-PCR. It possibly suggested that the high expression of TaGW8-B1 was positively associated with kernel size in bread wheat. Distribution of TaGW8-B1 allele indicated that TaGW8-B1a has been positively selected in Chinese wheat.

Genome-wide association mapping of grain yield in a diverse collection of spring wheat (Triticum aestivum L.) evaluated in southern Australia

Wheat landraces, wild relatives and other 'exotic' accessions are important sources of new favorable alleles. The use of those exotic alleles is facilitated by having access to information on the association of specific genomic regions with desirable traits. Here, we conducted a genome-wide association study (GWAS) using a wheat panel that includes landraces, synthetic hexaploids and other exotic wheat accessions to identify loci that contribute to increases in grain yield in southern Australia. The 568 accessions were grown in the field during the 2014 and 2015 seasons and measured for plant height, maturity, spike length, spike number, grain yield, plant biomass, HI and TGW. We used the 90K SNP array and two GWAS approaches (GAPIT and QTCAT) to identify loci associated with the different traits. We identified 17 loci with GAPIT and 25 with QTCAT. Ten of these loci were associated with known genes that are routinely employed in marker assisted selection such as Ppd-D1 for maturity and Rht-D1 for plant height and seven of those were detected with both methods. We identified one locus for yield per se in 2014 on chromosome 6B with QTCAT and three in 2015, on chromosomes 4B and 5A with GAPIT and 6B with QTCAT. The 6B loci corresponded to the same region in both years. The favorable haplotypes for yield at the 5A and 6B loci are widespread in Australian accessions with 112 out of 153 carrying the favorable haplotype at the 5A locus and 136 out of 146 carrying the favorable haplotype at the 6A locus, while the favorable haplotype at 4B is only present in 65 out of 149 Australian accessions. The low number of yield QTL in our study corroborate with other GWAS for yield in wheat, where most of the identified loci have very small effects.

The genome-wide transcriptional consequences of the nullisomic-tetrasomic stocks for homoeologous group 7 in bread wheat

Background

Hexaploid bread wheat (Triticum aestivum L) arose by two polyploidisation events from three diploid species with homoeologous genomes. Nullisomic-tetrasomic (nulli-tetra or NT) lines are aneuploid wheat plants lacking two and adding two of six homoeologous chromosomes. These plants can grow normally, but with significantly morphological variations because the adding two chromosomes or the remaining four chromosomes compensate for those absent. Despite these interesting phenomena, detailed molecular mechanisms underlying dosage deletion and compensation in these useful genetic materials have not been determined.

Results

By sequencing the transcriptomes of leaves in two-week-old seedlings, we showed that the profiles of differentially expressed genes between NT stocks for homoeologous group 7 and the parent hexaploid Chinese Spring (CS) occurred throughout the whole genome with a subgenome and chromosome preference. The deletion effect of nulli-chromosomes was compensated partly by the tetra-chromosomes via the dose level of expressed genes, according to the types of homoeologous genes. The functions of differentially regulated genes primarily focused on carbon metabolic process, photosynthesis process, hormone metabolism, and responding to stimulus, and etc., which might be related to the defective phenotypes that included reductions in plant height, flag leaf length, spikelet number, and kernels per spike.

Conclusions

The perturbation of the expression levels of transcriptional genes among the NT stocks for homoeologous group 7 demonstrated the gene dosage effect of the subgenome at the genome-wide level. The gene dosage deletion and compensation can be used as a model to elucidate the functions of the subgenomes in modern polyploid plants.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5421-3) contains supplementary material, which is available to authorized users.

Validation of Candidate Gene-Based Markers and Identification of Novel Loci for Thousand-Grain Weight in Spring Bread Wheat

Increased thousand-grain weight (TGW) is an important breeding target for indirectly improving grain yield (GY). Fourteen reported candidate genes known to enhance TGW were evaluated in two independent and existing datasets of wheat at CIMMYT, the Elite Yield Trial (EYT) from 2015 to 2016 (EYT2015-16) and the Wheat Association Mapping Initiative (WAMI) panel, to study their allele effects on TGW and to verify their suitability for marker-assisted selection. Of these, significant associations were detected for only one gene (TaGs3-D1) in the EYT2015-16 and two genes (TaTGW6 and TaSus1) in WAMI. The reported favorable alleles of TaGs3-D1 and TaTGW6 genes decreased TGW in the datasets. A haplotype-based genome wide association study was implemented to identify the genetic determinants of TGW on a large set of CIMMYT germplasm (4,302 lines comprising five EYTs), which identified 15 haplotype blocks to be significantly associated with TGW. Four of them, identified on chromosomes 4A, 6A, and 7A, were associated with TGW in at least three EYTs. The locus on chromosome 6A (Hap-6A-13) had the largest effect on TGW and additionally GY with increases of up to 2.60 g and 258 kg/ha, respectively. Discovery of novel TGW loci described in our study expands the opportunities for developing diagnostic markers and for multi-gene pyramiding to derive new allele combinations for enhanced TGW and GY in CIMMYT wheat.

Gene editing and mutagenesis reveal inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat

KEY MESSAGE

CRISPR-Cas9-based genome editing and EMS mutagenesis revealed inter-cultivar differences and additivity in the contribution of TaGW2 homoeologues to grain size and weight in wheat. The TaGW2 gene homoeologues have been reported to be negative regulators of grain size (GS) and thousand grain weight (TGW) in wheat. However, the contribution of each homoeologue to trait variation among different wheat cultivars is not well documented. We used the CRISPR-Cas9 system and TILLING to mutagenize each homoeologous gene copy in cultivars Bobwhite and Paragon, respectively. Plants carrying single-copy nonsense mutations in different genomes showed different levels of GS/TGW increase, with TGW increasing by an average of 5.5% (edited lines) and 5.3% (TILLING mutants). In any combination, the double homoeologue mutants showed higher phenotypic effects than the respective single-genome mutants. The double mutants had on average 12.1% (edited) and 10.5% (TILLING) higher TGW with respect to wild-type lines. The highest increase in GS and TGW was shown for triple mutants of both cultivars, with increases in 16.3% (edited) and 20.7% (TILLING) in TGW. The additive effects of the TaGW2 homoeologues were also demonstrated by the negative correlation between the functional gene copy number and GS/TGW in Bobwhite mutants and an F2 population. The highest single-genome increases in GS and TGW in Paragon and Bobwhite were obtained by mutations in the B and D genomes, respectively. These inter-cultivar differences in the phenotypic effects between the TaGW2 gene homoeologues coincide with inter-cultivar differences in the homoeologue expression levels. These results indicate that GS/TGW variation in wheat can be modulated by the dosage of homoeologous genes with inter-cultivar differences in the magnitude of the individual homoeologue effects.

Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers

We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay. Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai × Shi 4185 (D × S), Gaocheng 8901 × Zhoumai 16 (G × Z) and Linmai 2 × Zhong 892 (L × Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5-32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY.

Analysis of the functions of TaGW2 homoeologs in wheat grain weight and protein content traits

GW2 is emerging as a key genetic determinant of grain weight in cereal crops; it has three homoeologs (TaGW2-A1, -B1 and -D1) in hexaploid common wheat (Triticum aestivum L.). Here, by analyzing the gene editing mutants that lack one (B1 or D1), two (B1 and D1) or all three (A1, B1 and D1) homoeologs of TaGW2, several insights are gained into the functions of TaGW2-B1 and -D1 in common wheat grain traits. First, both TaGW2-B1 and -D1 affect thousand-grain weight (TGW) by influencing grain width and length, but the effect conferred by TaGW2-B1 is stronger than that of TaGW2-D1. Second, there exists functional interaction between TaGW2 homoeologs because the TGW increase shown by a double mutant (lacking B1 and D1) was substantially larger than that of their single mutants. Third, both TaGW2-B1 and -D1 modulate cell number and length in the outer pericarp of developing grains, with TaGW2-B1 being more potent. Finally, TaGW2 homoeologs also affect grain protein content as this parameter was generally increased in the mutants, especially in the lines lacking two or three homoeologs. Consistent with this finding, two wheat end-use quality-related parameters, flour protein content and gluten strength, were considerably elevated in the mutants. Collectively, our data shed light on functional difference between and additive interaction of TaGW2 homoeologs in the genetic control of grain weight and protein content traits in common wheat, which may accelerate further research on this important gene and its application in wheat improvement.

TaAAP6-3B, a regulator of grain protein content selected during wheat improvement

BACKGROUND

The content of grain protein (GPC) in cereals is an important part of total protein in human food. Exploring and utilizing new GPC genes is one of the most effective approaches for wheat quality breeding.

RESULTS

Three homoeologues of TaAAP6(-3A, 3B, 3D)were cloned by homology cloning from OsAAP6.Temporal and spatial expression analysis showed that TaAAP6homoeologues were preferentially expressed in developing grains, and TaAAP6-3B may play a major role in regulating GPC in wheat. Association analysis indicated thatTaAAP6-3B-I is significantly correlated with higher GPC than that of TaAAP6-3B-II for 115 wheat lines in all five environments. TaAAP6-3B-I, the favored allele of TaAAP6-3B, was preferentially expressed in preliminary developing grain stage. Two functional markers were developed to discriminate 197F2populations and the result showed that TaAAP6-3B-I (high-protein content) was completely dominant. Two cis-regulatory elements appear to be associated with high GPC were found in the 5'UTR of TaAAP6-3B-I.The change of the TaAAP6-3B locus types indicated that the gene was subjected to selection pressures during long process of artificial selection.

CONCLUSIONS

TaAAP6-3B is a regulator of GPC and its favored allele TaAAP6-3B-I exhibits an obvious potential application in wheat high-GPC breeding.