Key message
Three major loci for pre-harvest sprouting tolerance (PHST) were mapped on chromosomes 1AL, 3BS, and 6BL, and two CAPS and one dCAPS markers were validated. Sixteen lines with favorable ...alleles and increased PHST were identified.
Pre-harvest sprouting (PHS) significantly affects wheat grain yield and quality. In the present study, the PHS tolerance (PHST) of 192 wheat varieties (lines) was evaluated by assessment of field sprouting, seed germination index, and period of dormancy in different environments. A high-density Illumina iSelect 90K SNP array was used to genotype the panel. A genome-wide association study (GWAS) based on single- and multi-locus mixed linear models was used to detect loci for PHST. The single-locus model identified 23 loci for PHST (
P
< 0.0001) and explained 6.0–18.9% of the phenotypic variance. Twenty loci were consistent with known quantitative trait loci (QTLs). Three single-nucleotide polymorphism markers closely linked with three major loci (
Qphs.ahau-1A
,
Qphs.ahau-3B
, and
Qphs.ahau-6B
) on chromosomes 1AL, 3BS, and 6BL, respectively, were converted to two cleaved amplified polymorphic sequences (CAPS) and one derived-CAPS markers, and validated in 374 wheat varieties (lines). The CAPS marker EX06323 for
Qphs.ahau-6B
co-segregated with a novel major QTL underlying PHST in a recombinant inbred line population raised from the cross Jing 411 × Wanxianbaimaizi. Linear regression showed a clear dependence of PHST on the number of favorable alleles. Sixteen varieties showing an elevated degree of PHST were identified and harbored more than 16 favorable alleles. The multi-locus model detected 39 marker–trait associations for PHST (
P
< 0.0001), of which five may be novel. Six loci common to the two models were identified. The combination of the two GWAS methods contributes to efficient dissection of the complex genetic mechanism of PHST.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Heat shock transcription factors (Hsfs) play multifaceted roles in plant growth, development, and responses to environmental factors. However, their involvement in seed dormancy and germination ...processes has remained elusive. In this study, we identified a wheat class B Hsf gene, TaHsf-7A, with higher expression in strong-dormancy varieties compared to weak-dormancy varieties during seed imbibition. Specifically, TaHsf-7A expression increased during seed dormancy establishment and subsequently declined during dormancy release. Through the identification of a 1-bp insertion (ins)/deletion (del) variation in the coding region of TaHsf-7A among wheat varieties with different dormancy levels, we developed a CAPS marker, Hsf-7A-1319, resulting in two allelic variations: Hsf-7A-1319-ins and Hsf-7A-1319-del. Notably, the allele Hsf-7A-1319-ins correlated with a reduced seed germination rate and elevated dormancy levels, while Hsf-7A-1319-del exhibited the opposite trend across 175 wheat varieties. The association of TaHsf-7A allelic status with seed dormancy and germination levels was confirmed in various genetically modified species, including Arabidopsis, rice, and wheat. Results from the dual luciferase assay demonstrated notable variations in transcriptional activity among transformants harboring distinct TaHsf-7A alleles. Furthermore, the levels of abscisic acid (ABA) and gibberellin (GA), along with the expression levels of ABA and GA biosynthesis genes, showed significant differences between transgenic rice lines carrying different alleles of TaHsf-7A. These findings represent a significant step towards a comprehensive understanding of TaHsf-7A's involvement in the dormancy and germination processes of wheat seeds.
•The class B Hsf gene TaHsf-7A is highly expressed in wheat grains.•Transgenic experiments confirmed TaHsf-7A's crucial role in seed dormancy regulation.•AtHsfB2b and TaHsf-7A have functional similarity in regulating seed dormancy.•TaHsf-7A is involved in the ABA and GA signaling pathways to regulate seed dormancy.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Stripe rust, caused by
Puccinia striiformis
f. sp.
tritici
(
Pst
), is an important disease of wheat worldwide. Host resistance is the best way to control the disease. Genetic analysis of F
2
and F
...2:3
populations from an Avocet S/Jimai 22 cross indicated that stripe rust resistance in Jimai 22 was conferred by a single dominant gene, tentatively designated
YrJ22
. A total of 377 F
2
plants and 127 F
2:3
lines were tested with Chinese
Pst
race CYR32 and genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. A linkage map was constructed with five SSR and two SNP markers.
Xwmc658
and
IWA1348
flanked
YrJ22
at genetic distances of 1.0 and 7.3 cM, proximally and distally, respectively. The chromosomal location was confirmed using Chinese Spring nulli-tetrasomic, ditelosomics and deletion lines. Seedling reactions to 21
Pst
races demonstrated differences in specificity between
YrJ22
and other resistance genes on chromosome 2AL, indicating that
YrJ22
is likely to be a new wheat stripe rust resistance gene.
Heat stress is one of the major threats to wheat production in many wheat-growing areas of the world as it causes severe yield loss at the reproductive stage. In the current study, 28 crosses were ...developed using 11 parental lines, including 7 female lines and 4 male testers following line × tester matting design in 2018–2019. Twenty-eight crosses along with their 11 parental lines were sown in a randomized complete block design in triplicate under optimal and heat stress conditions. Fifteen different morpho-physiological and grain quality parameters were recorded at different growth stages. Analysis of variance illustrated the presence of highly significant differences among wheat genotypes for all traits under both optimal and heat stress conditions. The results of combining ability unveiled the predominant role of non-additive gene action in the inheritance of almost all the studied traits under both conditions. Among parents, 3 parental lines WL-27, WT-39, and WL-57 showed good combining ability under both normal and heat stress conditions. Among crosses, WL-8 × WT-17, WL-37 × WT-17, WL-7 × WT-39, and WL-37 × WT-39 portrayed the highest specific combining ability effects for grain yield and its related traits under optimal as well as heat stress conditions. Biplot and cluster analysis confirmed the results of general and specific combining ability by showing that these wheat crosses belonged to a highly productive and heat tolerant cluster. Correlation analysis revealed a significantly positive correlation of grain yield with net photosynthetic rate, thousand-grain rate, and the number of grains per spike. The designated parental lines and their crosses were selected for future breeding programs in the development of heat resilient, climate-smart wheat genotypes.
Key message
A new stripe rust resistance gene
YrBDT
in Chinese landrace wheat Baidatou was mapped to a 943.6-kb interval on chromosome arm 6DS and co-segregated with a marker
CAPS3
developed from ...candidate gene
TraesCS6D03G0027300.
Stripe rust caused by
Puccinia striiformis
f. sp.
tritici
(
Pst
) is a devastating foliar disease of wheat. Chinese landrace wheat Baidatou has shown high resistance to a broad spectrum of
Pst
races at both the seedling and adult-plant stages for decades in the Longnan region of Gansu province, a hot spot for stripe rust epidemics. Here, we report fine mapping and candidate gene analysis of stripe rust resistance gene
YrBDT
in Baidatou. Analysis of F
1
, F
2
plants and F
2:3
lines indicated that resistance in Baidatou to
Pst
race CYR31 was conferred by a single dominant gene, temporarily designated
YrBDT
. Bulked segregant exome capture sequencing (BSE-seq) analysis revealed 61 high-confidence polymorphic SNPs concentrated in a 5.4-Mb interval at the distal of chromosome arm 6DS. Several SNPs and InDels were also identified by genome mining of DNA sampled from the parents and contrasting bulks. The
YrBDT
locus was mapped to a 943.6-kb (4,658,322–5,601,880 bp) genomic region spanned by markers
STS2
and
STS3
based on IWGSC RefSeq v2.1, including five putative disease resistance genes. There was high collinearity of the target interval among Chinese Spring RefSeq v2.1,
Ae
.
tauschii
AL8/78 and Fielder genomes. The expression level of
TraesCS6D03G0027300
showed significant association with
Pst
infection, and a gene-specific marker
CAPS3
developed from
TraesCS6D03G0027300
co-segregated with
YrBDT
suggesting this gene as a candidate of
YrBDT
. The resistance gene and flanking markers can be used in marker-assisted selection for improvement of stripe rust resistance.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Calcium-dependent protein kinases (CPKs), important sensors of calcium signals, play an essential role in plant growth, development, and stress responses. Although the CPK gene family has been ...characterized in many plants, the functions of the CPK gene family in wheat, including their relationship to seed dormancy and germination, remain unclear. In this study, we identified 84 TaCPK genes in wheat (TaCPK1-84). According to their phylogenetic relationship, they were divided into four groups (I-IV). TaCPK genes in the same group were found to have similar gene structures and motifs. Chromosomal localization indicated that TaCPK genes were unevenly distributed across 21 wheat chromosomes. TaCPK gene expansion occurred through segmental duplication events and underwent strong negative selection. A large number of cis-regulatory elements related to light response, phytohormone response, and abiotic stress response were identified in the upstream promoter sequences of TaCPK genes. TaCPK gene expression was found to be tissue- and growth-stage-diverse. Analysis of the expression patterns of several wheat varieties with contrasting seed dormancy and germination phenotypes resulted in the identification of 11 candidate genes (TaCPK38/-40/-43/-47/-50/-60/-67/-70/-75/-78/-80) which are likely associated with seed dormancy and germination. The ectopic expression of TaCPK40 in Arabidopsis promoted seed germination and reduced abscisic acid (ABA) sensitivity during germination, indicating that TaCPK40 negatively regulates seed dormancy and positively regulates seed germination. These findings advance our understanding of the multifaceted functions of CPK genes in seed dormancy and germination, and provide potential candidate genes for controlling wheat seed dormancy and germination.
•84 CPK genes were identified in wheat and classified into four groups.•Eleven wheat CPK candidate genes may help regulate seed dormancy and germination.•Overexpression TaCPK40 in Arabidopsis negatively regulates seed dormancy and positively regulates seed germination.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
C3H zinc finger transcription factors play important roles in managing various biotic/abiotic stresses in Aarabidopsis, rice, and maize. The functions of these factors in wheat, however, remain ...largely unclear. We identified 88 TaC3H genes that were divided into four subfamilies in this analysis. Gene structure and conserved domain analyses indicate that most members of the same subfamily have similar structures. A total of 76 paralogous and 48 orthologous pairs were identified and Ka/Ks values were used to analyze replication relationships amongst wheat, rice, and Arabidopsis. Gene ontology (GO) annotation analysis showed that most TaC3H genes possessed molecular functions, while transcriptome results showed that the 88 TaC3H genes responded to water imbibition. Microarray data for 53 TaC3H genes were obtained and heat maps were generated; these results indicate that these genes are expressed in 13 wheat tissues. Subcellular localization prediction analysis indicates that most TaC3H genes are located in the nucleus. Promoter analysis indicates that most TaC3H genes contained cis-elements including ABRE, GARE-motif, and MBS, indicating that these can respond to various biotic/abiotic stresses. Transcriptome data and quantitative real-time PCR analysis of wheat cultivars with contrasting seed dormancy phenotypes show that five genes TaC3H4/-18/-37/-51/-72 were very likely involved in seed dormancy and germination. Exogenous ABA treatment further indicated that these five genes were responsive to ABA, suggesting that there may be a crosstalk between these genes and ABA signaling pathway in controlling seed dormancy and germination. These results provide a theoretical basis for subsequent studies on TaC3H gene function and also contribute to studies on the C3H gene in other species.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Late embryogenesis abundant (LEA) proteins play important roles in plant development and responses to diverse stresses. However, their specific roles in seed dormancy and germination remain unclear. ...In this study, we identified TaLEA-1A, an LEA gene highly expressed in wheat seeds and differentially expressed in imbibed seeds of weak-dormancy variety Jing 411 (J411) and strong-dormancy variety Hongmangchun 21 (HMC21). Sequence analyses revealed 14 variations in the promoter and coding regions of TaLEA-1A between J411 and HMC21. Subsequent validation established associations of a single nucleotide polymorphism (SNP) in the promoter (-1366 bp, G/A) and an insertion/deletion (Indel) variation in the coding region (+345 bp, -/C) with seed dormancy and germination across 192 wheat varieties. Furthermore, the effects of the strong-dormancy allele TaLEA-1A-345-ins and weak-dormancy allele TaLEA-1A-345-del on seed dormancy and germination were confirmed using transgenic Arabidopsis and rice lines as well as J411 mutant induced with ethyl methane sulphonate. Analyses of endogenous hormone contents and expression patterns suggested that TaLEA-1A may regulate seed dormancy and germination by mediating gibberellic acid and abscisic acid balance. These findings not only contribute to unraveling the intricate regulatory network governing seed dormancy and germination in wheat and other plants but also provide a favorable gene and molecular marker for genetic improvement of wheat PHS resistance.
•Role of wheat Late embryogenesis abundant gene TaLEA-1A in seed germination and dormancy.•Discovery of a superior haplotype of TaLEA-1A for PHS resistance in wheat.•We verified the role of TaLEA-1A in seed dormancy and germination using transgenic Arabidopsis and rice materials, along with a wheat EMS mutant.•TaLEA-1A may regulate seed dormancy and germination by affecting GA and ABA metabolism and signal transduction pathways.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
GATA transcription factors have been reported to function in plant growth and development and during various biotic/abiotic stresses in Arabidopsis and rice. However, the functions of wheat GATAs, ...particularly in the regulation of seed dormancy and germination, remain unclear. Here, we identified 78 TaGATAs in wheat and divided them into five subfamilies. Sixty-four paralogous pairs and 52 orthologous pairs were obtained, and Ka/Ks ratios showed that the TaGATAs had undergone strong purifying election during the evolutionary process. Triplet analysis indicated that a high homologue retention rate could explain the large number of TaGATAs in wheat. Gene structure analysis revealed that most members of the same subfamily had similar structures, and subcellular localization prediction indicated that most TaGATAs were located in the nucleus. Gene ontology annotation results showed that most TaGATAs had molecular functions in DNA and zinc binding, and promoter analysis suggested that they may play important roles in growth, development, and biotic/abiotic stress response. We combined three microarray datasets with qRT-PCR expression data from wheat varieties of contrasting dormancy and pre-harvest sprouting resistance levels during imbibition in order to identify ten candidate genes (TaGATA17/-25/-34/-37/-40/-46/-48/-51/-72/-73) that may be involved in the regulation of seed dormancy and germination in wheat. These findings provide valuable information for further dissection of TaGATA functions in the regulation of seed dormancy and germination, thereby enabling the improvement of wheat pre-harvest sprouting resistance by gene pyramiding.
•78 GATA members were identified in wheat, whose Arabidopsis homologs include important dormancy-related genes such as CO, GNC, and GNL.•Ten TaGATA candidates gene were likely to influence seed germination and dormancy in wheat.•Our findings provide useful information for our understanding of GATA functions in crops and plants.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Global warming is primarily characterized by asymmetric temperature increases, with higher temperature rises in winter/spring and at night compared to summer/autumn and daytime. We investigated the ...impact of winter night warming on wheat leaves using the spring wheat cultivar Yangmai 18 and the semi-winter wheat cultivar Yannong 19 during the 2020–2021 growing season. This study aimed to examine the effect of winter night warming on the top expanded leaf of wheat plants. The results showed that the night mean temperature in the treatment group increased by 1.27°C compared to the ambient temperature and winter night warming increased the yield of both wheat cultivars, the activities of sucrose synthase and sucrose phosphate synthase after anthesis, and the biosynthesis of sucrose and soluble sugars. The differentially expressed genes were identified using P-value<0.05 and fold change>2, and subjected to Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. The genes differentially expressed in wheat leaves treated with night warming were primarily associated with starch and sucrose metabolism, amino acid biosynthesis, carbon metabolism, plant hormone signal transduction, and amino sugar and nucleotide sugar metabolism. Comparison between groups identified 14 differentially expressed genes related to temperature. These results highlight the effects of winter night warming on wheat development from various perspectives. Our results provide new insights into the molecular mechanisms of the wheat response to winter night warming and the candidate genes involved in this process.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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