Traits In Common Wheat Research Articles

Functional Characterization of Accessible Chromatin in Common Wheat.

Eukaryotic gene transcription is fine-tuned by precise spatiotemporal interactions between cis-regulatory elements (CREs) and trans-acting factors. However, how CREs individually or coordinated with epigenetic marks function in regulating homoeolog bias expression is still largely unknown in wheat. In this study, through comprehensively characterizing open chromatin coupled with DNA methylation in the seedling and spikelet of common wheat, we observed that differential chromatin openness occurred between the seedling and spikelet, which plays important roles in tissue development through regulating the expression of related genes or through the transcription factor (TF)-centered regulatory network. Moreover, we found that CHH methylation may act as a key determinant affecting the differential binding of TFs, thereby resulting in differential expression of target genes. In addition, we found that sequence variations in MNase hypersensitive sites (MHSs) result in the differential expression of key genes responsible for important agronomic traits. Thus, our study provides new insights into the roles of CREs in regulating tissue or homoeolog bias expression, and controlling important agronomic traits in common wheat. It also provides potential CREs for genetic and epigenetic manipulation toward improving desirable traits for wheat molecule breeding.

Analysis of the Effects of the Vrn-1 and Ppd-1 Alleles on Adaptive and Agronomic Traits in Common Wheat (Triticum aestivum L.).

Wheat heading time is primarily governed by two loci: VRN-1 (response to vernalization) and PPD-1 (response to photoperiod). Five sets of near-isogenic lines (NILs) were studied with the aim of investigating the effect of the aforementioned genes on wheat vegetative period duration and 14 yield-related traits. Every NIL was sown in the hydroponic greenhouse of the Institute of Cytology and Genetics, SB RAS. To assess their allelic composition at the VRN-1 and PPD-1 loci, molecular markers were used. It was shown that HT in plants with the Vrn-A1vrn-B1vrn-D1 genotype was reduced by 29 and 21 days (p < 0.001) in comparison to HT in plants with the vrn-A1Vrn-B1vrn-D1 and the vrn-A1vrn-B1Vrn-D1 genotypes, respectively. In our study, we noticed a decrease in spike length as well as spikelet number per spike parameter for some NIL carriers of the Vrn-A1a allele in comparison to carriers of the Vrn-B1 allele. PCA revealed three first principal components (PC), together explaining more than 70% of the data variance. Among the studied genetic traits, the Vrn-A1a and Ppd-D1a alleles showed significant correlations with PCs. Regarding genetic components, significant correlations were calculated between PC3 and Ppd-B1a (-0.26, p < 0.05) and Vrn-B1 (0.57, p < 0.05) alleles. Thus, the presence of the Vrn-A1a allele affects heading time, while Ppd-D1a is associated with plant height reduction.

Effect of a novel dwarfing mutant site on chromosome 4B on agronomic traits in common wheat.

The introduction of dwarfing genes triggered a wave of "green revolution". A number of wheats dwarfing genes have been reported in previous studies, and only a small fraction of these have been applied to production practices. Therefore, the development of novel dwarfing genes for wheat is of great value. In this study, a novel dwarfing site, Rht-yz, identified in the Yanzhan mutation, is located on chromosome 4B (30-33MB) and its mechanism of action is different from that of Rht-B1b (C-T mutation), but whether it affects the Rht-B1a (TraesCS4B02G043100) or other genes is unclear. Exogenously applied GA3 experiments showed that Rht-yz is one of the gibberellin-insensitive dwarf genes. The effects of the dwarf gene Rht-yz on agronomic traits in wheat were evaluated in the field using Yanzhan, Yanzhan mutations, F2:3 and F3:4 lines. The results showed that Rht-yz improved lodging resistance by reducing plant height, increasing diameter, wall thickness and mechanical strength of the basal stem. In terms of yield traits, Rht-yz had negative effects on tiller number plant-1, biomass plant-1 and yield plant-1, but had no significant effect on harvest index, 1000-kernel weight and spike traits. In addition, Rht-yz significantly increased crude protein, wet gluten and starch content. Therefore, the rational use of the new dwarfing site Rht-yz has potential and value in dwarf wheat breeding.

Associations between allelic differences of the fifth group chromosome loci and a complex of agronomically valuable traits in common wheat (Triticum aestivum L.)

Aim. Characterization of recombinant inbred wheat lines by agronomically relevant traits and detection of asso- ciations between their expression level and allelic differences of microsatellite loci of the fifth group chromosomes. Methods. Phenological observations, morphometric indicators, and elements of crop structure. Statistical analysis of the obtained data was carried out in Microsoft Excel. The significance of the difference between samples was assessed by Fisher’s F test. A difference of p &lt; 0.05 was considered statistically significant for all indicators. Results. The poly- morphism of the parental genotypes and the population of 47 recombinant-inbred lines (RILs) F7 from the crossing of the winter wheat varieties Luzanivka odeska and Odeska chervonokolosa over three years (2016–2018) in conditions of the Southern Steppe (Odesa) was evaluated according to eight characteristics: duration of a period prior to heading, plant height, productive tillering, grain number per spike, grain weight per spike, thousand-grain weight, productive tiller number per unit area and grain yield. The comparison of the data of line evaluation by agronomic traits against the data of microsatellite analysis of lines by 14 microsatellite loci of the fifth group chromosomes demonstrated the associations between several loci and grain yield and between two loci and plant height. Conclusions. The changes in grain yield in the most unfavorable year, 2018, were associated with allelic differences of lines at locus Xbarc319- 5A, and in the most favorable year, 2017, – with another locus of chromosome 5A, Xbarc330-5A. In both cases, the lines that had an allele from Odeska chervonokolosa were characterized by a significantly higher level of grain yield compared to the lines that had an allele from the Luzanivka odeska variety. There are at least two QTLs on 5B chromo- some, associated with winter wheat grain yield in favorable growing years. The first of them is located in the region of locus Xbarc88-5B, and the second – in the region of loci Xwmc415-5B, Xgpw3191-5B, and Xcfd7-5B. Based on the alleles of the specified microsatellite loci, which are linked QTLs of grain yield, it is possible to select genotypes at the early stages of selection that will give a higher yield in years with favorable conditions for growing wheat.

Mapping QTLs with additive and epistatic effects for awn length and their effects on kernel-related traits in common wheat.

Wheat awns are crucial determinants of wheat yield due to their capacity to photosynthesize and exchange gas. Understanding the genetic basis of awn length (AL) is essential for improving wheat yield in molecular breeding programs. In this study, quantitative trait loci (QTLs) of AL were analyzed using recombinant inbred line (RIL) mapping population referred to as YY-RILs, which was derived from a cross between Yannong 15 (YN15) and Yannong 1212 (YN1212). Seven putative additive QTLs and 30 pairwise epistatic QTLs for AL were identified. Among them, five novel additive QTLs (except qAl-2A and qAl-5A.2) and 30 novel pairwise epistatic QTLs were identified. qAl-5A.1 was repeatedly identified in all five environment datasets, which was considered to be one novel stable QTL for AL with minor additive effects. eqAl-2B.2-2 significantly interacted with eight loci and could be of great importance in regulating awn development. The genes associated with the major stable QTL of qAl-5A.2 and the minor stable QTL of qAl-2A were B1 and WFZP-A, respectively. Awn lengths exhibited significant genetic correlations with kernel weight and kernels per spike, which could affect grain protein content to a lesser extent. This study enhances our understanding of the genetic basis of awn development and identifies novel genes as well as markers for future genetic improvement of wheat yield.

Genome-wide association study of seedling nitrogen-use efficiency-associated traits in common wheat (Triticum aestivum L.)

Nitrogen (N) fertilizer application is essential for crop-plant growth and development. Identifying genetic loci associated with N-use efficiency (NUE) could increase wheat yields and reduce environmental pollution caused by overfertilization. We subjected a panel of 389 wheat accessions to N and chlorate (a nitrate analog) treatments to identify quantitative trait loci (QTL) controlling NUE-associated traits at the wheat seedling stage. Genotyping the panel with a 660K single-nucleotide polymorphism (SNP) array, we identified 397 SNPs associated with N-sensitivity index and chlorate inhibition rate. These SNPs were merged into 49 QTL, of which eight were multi-environment stable QTL and 27 were located near previously reported QTL. A set of 135 candidate genes near the 49 QTL included TaBOX (F-box family protein) and TaERF (ethylene-responsive transcription factor). A Tabox mutant was more sensitive to low-N stress than the wild-type plant. We developed two functional markers for Hap 1, the favorable allele of TaBOX.

Genome-wide linkage mapping of root system architecture-related traits in common wheat (Triticum aestivum L.).

Identifying loci for root system architecture (RSA) traits and developing available markers are crucial for wheat breeding. In this study, RSA-related traits, including total root length (TRL), total root area (TRA), and number of root tips (NRT), were evaluated in the Doumai/Shi4185 recombinant inbred line (RIL) population under hydroponics. In addition, both the RILs and parents were genotyped using the wheat 90K single-nucleotide polymorphism (SNP) array. In total, two quantitative trait loci (QTLs) each for TRL (QTRL.caas-4A.1 and QTRL.caas-4A.2), TRA (QTRA.caas-4A and QTRA.caas-4D), and NRT (QNRT.caas-5B and QNRT.caas-5D) were identified and each explaining 5.94%-9.47%, 6.85%-7.10%, and 5.91%-10.16% phenotypic variances, respectively. Among these, QTRL.caas-4A.1 and QTRA.caas-4A overlapped with previous reports, while QTRL.caas-4A.2, QTRA.caas-4D, QNRT.caas-5B, and QNRT.caas-5D were novel. The favorable alleles of QTRL.caas-4A.1, QTRA.caas-4A, and QTRA.caas-5B were contributed by Doumai, whereas the favorable alleles of QTRL.caas-4A.2, QTRA.caas-4D, and QTRA.caas-5D originated from Shi 4185. Additionally, two competitive allele-specific PCR (KASP) markers, Kasp_4A_RL (QTRA.caas-4A) and Kasp_5D_RT (QNRT.caas-5D), were developed and validated in 165 wheat accessions. This study provides new loci and available KASP markers, accelerating wheat breeding for higher yields.

Evaluation of General and Specific Combining Ability for Yield and its Attributing Traits in Bread Wheat (Triticum aestivum L.)

In order to investigate the general and specific combining ability (GCA and SCA) and gene action for yield and its contributing traits in common wheat, 10 lines and 4 testers were crossed using line × tester mating design at the Crop Research Center of SVP University of Agriculture and Technology, Meerut, Uttar Pradesh, India. The experimental material was raised under Randomized Block Design with three repetitions during rabi season of 2019–20 and 2020–21. The variance due to cross vs parent was highly significant for all the traits. Estimates of SCA variance for harvest index, plant height, biological yield per plant, 1000 grain weight, days to 50% blooming, grain yield per plant, days to maturity and number of productive tillers per plant, were higher than those of GCA variance, depicting the prevalence of non-additive gene action. GCA variance was found to be higher than SCA variance for the remaining characteristics, reflecting additive gene action. Based on GCA four parents were found promising (UP1109, DBW187, HD3237, PBW226, RAJ3777). On the basis of SCA, 9 crosses (HD3237 × WR544, RAJ 3777 × HD3086, DBW187 × HD3086, DBW187 × PBW226, K9162 × WH1105, PBW373 × WH1105, K9162 × PBW226, UP2628 × WR544, UP1109 × PBW226) were identified good specific combiner for grain yield per plant. In present study non-additive type of gene action was more pronounced, which can be utilized by pedigree method, biparental mating and selection in later generation.

An improved in-vitro regeneration protocol using scutellum of mature and immature embryos of wheat

Generally, conventional practices take a long time to improve agronomic traits in common wheat (Triticum aestivum L.). However, biotechnological tools provide the best opportunity to enhance crop potential within a limited time. A simple and repeatable protocol for wheat regeneration is the priority for transforming the genetic makeup of elite wheat cultivars. Among 10 types of callus induction media (CIM), CIM4 with supplemented Murashige and Skoog (MS) media+ dicamba (2 mg/l) has 98.22 and 97.33% callus induction efficiency (CIE) in immature and mature scutellum, respectively. Precocious germination, considered a key barrier during callus induction, was fully controlled by excising the embryonic axis. Among 29 different shoot induction media (SIM) assessed in the study, SIM 29 containing zeatin 5 mg/l, 6-benzylaminopurine (BAP) 5 mg/l, 2,4-dichlorophenoxyacetic acid (2,4-D) 0.25 mg/l,1-naphthaleneacetic acid (NAA) 0.25 mg/l, and copper sulfate (CuSO4) 20 mg/l was found most responsive for shoot induction. The combined effect of cytokinin and CuSO4 resulted in an improved wheat regeneration response in two popular Indian wheat varieties, namely HD2967 and HD3171. Rooting was observed at 100% using IAA and IBA @ 0.2 mg/l concentration in root induction media (RIM). The whole in-vitro regeneration protocol from embryo to transfer in the greenhouse took 8 to 9 weeks. The in-vitro regeneration protocol developed in the present study could further be utilized to improve the genetic makeup of elite wheat cultivars utilizing genetic engineering tools.

Introgression of QTL from Aegilops tauschii enhances yield-related traits in common wheat

To break the narrow diversity bottleneck of the wheat D genome, a set of Aegilops tauschii-wheat introgression (A-WI) lines was developed by crossing Ae. tauschii accession T015 with common wheat elite cultivar Zhoumai 18 (Zhou18). A high-density genetic map was constructed based on Single Nucleotide Polymorphism (SNP) markers and 15 yield-related traits were evaluated in 11 environments for detecting quantitative trait loci (QTL). A total of 27 environmentally stable QTL were identified in at least five environments, 20 of which were derived from Ae. tauschii T015, explaining up to 24.27% of the phenotypic variations. The major QTL for kernel length (KL), QKl-2D.5, was delimited to a physical interval of approximately 2.6 Mb harboring 52 candidate genes. Three Kompetitive Allele Specific PCR (KASP) markers were successfully developed based on nonsynonymous nucleotide mutations of candidate gene AetT093_2Dv1G100900.1 and showed that A-WI lines with the T015 haplotype had significantly longer KL than the Zhou18 haplotype across all 11 environments. Four primary valuable A-WIs with good trait performance and carrying yield-related QTL were selected for breeding improvement. The results will facilitate the efficient transfer of beneficial genes from Ae. tauschii into wheat cultivars to improve wheat yield and other traits.

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.

Meta-QTL analysis and in-silico transcriptome assessment for controlling chlorophyll traits in common wheat.

Chlorophyll is an important plant molecule for absorbing light and transferring electrons to produce energy for photosynthesis, which has a significant impact on crop yield. To identify quantitative trait loci (QTL) controlling chlorophyll traits in wheat (Triticum aestivum L.), a comprehensive meta-analysis of 411 original QTLs for six chlorophyll traits was performed, including the evolution of soil plant analysis development (SPAD), chlorophyll content index (CCI), chlorophyll a content (Chla), chlorophyll b content (Chlb), chlorophyll content (Chl), and ratio of chlorophyll a to b (Chla/b), derived from 41 independent experiments conducted over the past two decades. Fifty-six consensus meta-QTLs (MQTLs) were detected, unevenly distributed on chromosomes 1A, 1B, 2A, 2B, 2D, 3B, 3D, 4B, 4D, 5A, 5D, 6A, 6D, 7B, and 7D. The confidence interval (CI) of the identified MQTLs was 0.18 to 15.07 cM, with an average of 5.74 cM, and 3.17-times narrower than that of the original QTLs. A total of 30 MQTLs were aligned with marker-trait associations (MTAs) reported in genome-wide association studies (GWAS) for chlorophyll traits in wheat. Based on MQTL-flanking marker information and homology analyses combined with RNA-seq data, 136 putative candidate genes were identified in MQTL regions, involved in porphyrin metabolism, photosynthesis, terpene biosynthesis, glyoxylate and dicarboxylate metabolism, and secondary metabolites. The results of this study contribute to the understanding of the genetic basis for controlling chlorophyll traits and can be used in breeding wheat with high photosynthetic efficiency.

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.

Rapid identification and deployment of major genes for flowering time and awn traits in common wheat.

Molecular markers are developed to accelerate deployment of genes for desirable traits segregated in a bi-parental population of recombinant inbred lines (RILs) or doubled haplotype (DH) lines for mapping. However, it would be the most effective if such markers for multiple traits could be identified in an F2 population. In this study, single nucleotide polymorphisms (SNP) chips were used to identify major genes for heading date and awn in an F2 population without developing RILs or DH lines. The population was generated from a cross between a locally adapted spring wheat cultivar “Ningmaizi119” and a winter wheat cultivar “Tabasco” with a diverse genetic background. It was found that the dominant Vrn-D1 allele could make Ningmaizi119 flowered a few months earlier than Tabasco in the greenhouse and without vernalization. The observed effects of the allele were validated in F3 populations. It was also found that the dominant Ali-A1 allele for awnless trait in Tabasco or the recessive ali-A1 allele for awn trait in Ningmaizi119 was segregated in the F2 population. The allelic variation in the ALI-A1 gene relies not only on the DNA polymorphisms in the promoter but also on gene copy number, with one copy ali-A1 in Ningmaizi119 but two copies Ali-A1 in Tabasco based on RT-PCR results. According to wheat genome sequences, cultivar “Mattis” has two copies Ali-A1 and cultivar “Spelta” has four copies Ali-A in a chromosome that was uncharacterized (ChrUN), in addition to one copy on chromosome 5A. This study rapidly characterized the effects of the dominant Vrn-D1 allele and identified the haplotype of Ali-A1 in gene copy number in the F2 segregation population of common wheat will accelerate their deployment in cycling lines in breeding.

Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

BackgroundSoil salinization is a major threat to wheat production. It is essential to understand the genetic basis of salt tolerance for breeding and selecting new salt-tolerant cultivars that have the potential to increase wheat yield.ResultIn this study, a panel of 191 wheat accessions was subjected to genome wide association study (GWAS) to identify SNP markers linked with adult-stage characters. The population was genotyped by Wheat660K SNP array and eight phenotype traits were investigated under low and high salinity environments for three consecutive years. A total of 389 SNPs representing 11 QTLs were significantly associated with plant height, spike number, spike length, grain number, thousand kernels weight, yield and biological mass under different salt treatments, with the phenotypic explanation rate (R2) ranging from 9.14 to 50.45%. Of these, repetitive and pleiotropic loci on chromosomes 4A, 5A, 5B and 7A were significantly linked to yield and yield related traits such as thousand kernels weight, spike number, spike length, grain number and so on under low salinity conditions. Spike length-related loci were mainly located on chromosomes 1B, 3B, 5B and 7A under different salt treatments. Two loci on chromosome 4D and 5A were related with plant height in low and high salinity environment, respectively. Three salt-tolerant related loci were confirmed to be important in two bi-parental populations. Distribution of favorable haplotypes indicated that superior haplotypes of pleiotropic loci on group-5 chromosomes were strongly selected and had potential for increasing wheat salt tolerance. A total of 14 KASP markers were developed for nine loci associating with yield and related traits to improve the selection efficiency of wheat salt-tolerance breeding.ConclusionUtilizing a Wheat660K SNPs chip, QTLs for yield and its related traits were detected under salt treatment in a natural wheat population. Important salt-tolerant related loci were validated in RIL and DH populations. This study provided reliable molecular markers that could be crucial for marker-assisted selection in wheat salt tolerance breeding programs.

Utilization of a Wheat55K SNP array-derived high-density genetic map for high-resolution mapping of quantitative trait loci for important kernel-related traits in common wheat.

This study mapped QTLs associated with kernel-related traits by high-density genetic map. Five new major and stable QTLs for KL, KDR, SN, and KWPS were mapped in multiple environments. In the present study, a recombinant inbred line population including 371 lines derived from the cross of Chuannong18 and T1208 was genotyped using the Wheat55K single nucleotide polymorphism array. A novel high-density genetic map consisting of 11,583 markers spanning 4192.62cM and distributed across 21 wheat chromosomes was constructed. QTLs for important kernel-related traits were mapped in multiple environments. A total of 96 and 151 QTLs were mapped by using the ICIM method and the MET method, respectively. And a total of 114 digenic epistatic QTLs were also detected across 21 chromosomes, and the epistatic effects of each trait were analyzed. BLAST analysis showed that 23QTLs for different kernel-related traits were first time mapped and five of them were major and stable QTLs for kernel diameter ratio (121.34-126.83cM on 4BS), spike number per square meter (71.32-73.84cM on 2DS), kernel weight per spike (71.32-75.26cM on 2DS), and kernel length (16.78-31.64cM on 6A and 51.63-58.40cM on 3D), respectively. FifteenQTL clusters that contained 58 QTLs were also detected, and all most stable QTLs were contained in these QTL clusters. Significant correlations between different traits were detected and discussed. These results lay the foundation for fine mapping and cloning of the gene(s) underlying the stable QTLs detected in this study.

Characterization of near-isogenic lines confirmed QTL and revealed candidate genes for plant height and yield-related traits in common wheat.

The online version contains supplementary material available at 10.1007/s11032-020-01196-8.

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

BackgroundKernel 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.ResultsIn 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.ConclusionsSeventeen 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.

Genome-wide association study of six quality-related traits in common wheat (Triticum aestivum L.) under two sowing conditions

We identified genomic regions associated with six quality-related traits in wheat under two sowing conditions and analyzed the effects of multienvironment-significant SNPs on the stability of these traits. Grain quality affects the nutritional and commercial value of wheat (Triticum aestivum L.) and is a critical factor influencing consumer preferences for specific wheat varieties. Climate change is predicted to increase environmental stress and thereby reduce wheat quality. Here, we performed a genotyping assay involving the use of the wheat 90K array in a genome-wide association study of six quality-related traits in 486 wheat accessions under two sowing conditions (normal and late sowing) over 4years. We identified 64 stable quantitativetrait loci (QTL), including 10 for grain protein content, 9 for wet gluten content, 4 for grain starch content, 14 for water absorption, 15 for dough stability time and 12 for grain hardness in wheat under two sowing conditions. These QTL harbored 175 single nucleotide polymorphisms (SNPs), explaining approximately 3-13% of the phenotypic variation in multiple environments. Some QTL on chromosomes 6A and 5D were associated with multiple traits simultaneously, and two (QNGPC.cau-6A, QNGH.cau-5D) harbored known genes, such as NAM-A1 for grain protein content and Pinb for grain hardness, whereas other QTL could facilitate gene discovery. Forty-three SNPs that were detected under late or both normal and late sowing conditions appear to be related to phenotypic stability. The effects of these SNP alleles were confirmed in the association population. The results of this study will be useful for further dissecting the genetic basis of quality-related traits in wheat and developing new wheat cultivars with desirable alleles to improve the stability of grain quality.

MiR164-targeted TaPSK5 encodes a phytosulfokine precursor that regulates root growth and yield traits in common wheat (Triticum aestivum L.)

TaPSK5 is a less conserved target of miR164 in wheat encoding a positive regulator of root growthand yield traits that could be used for crop improvement. MicroRNAs (miRNAs) play key roles in regulating plant growth and development by targeting the mRNAs of conserved genes. However, little is known about the roles of less conserved miRNA-targeted genes in plants. In the current study, we identified TaPSK5, encoding a phytosulfokine precursor, as a novel target of miR164. Compared with miR164-targeted NAC transcription factor genes, TaPSK5 is less conserved between monocots and dicots. Expression analysis indicated that TaPSK5 homoeologs were constitutively expressed in wheat tissues, especially young spikes. Overexpression of TaPSK5-D and miR164-resistant TaPSK5-D (r-TaPSK5-D) led to increased primary root growth and grain yield in rice, with the latter having more significant effects. Comparison of the transcriptome between wild-type and r-TaPSK5-D overexpression plants revealed multiple differentially expressed genes involved in hormone signaling, transcription regulation, and reactive oxygen species (ROS) homeostasis. Moreover, we identified three TaPSK5-A haplotypes (TaPSK5-A-Hap1/2/3) and two TaPSK5-B haplotypes (TaPSK5-B-Hap1/2) in core collections of Chinese wheat. Both TaPSK5-A-Hap1 and TaPSK5-B-Hap2 are favorable haplotypes associated with superior yield traits that were under positive selection during wheat breeding. Together, our findings identify miR164-targeted TaPSK5 as a regulator of root growth and yield traits in common wheat with potential applications for the genetic improvement of crops.