Identification of loci for pre-harvest sprouting resistance in the highly dormant spring wheat RL4137

The ethylene responsive factor TaERF-2 A activates gibberellin 2-oxidase gene TaGA2ox2-3B expression to enhance seed dormancy in wheat

The plant hormone gibberellin (GA) plays a key role in breaking seed dormancy, but the underlying regulatory mechanism is not fully understood. Here, we reported TraesCS3B02G166100 (named TaGA2ox2-3B), encoding a GA metabolism enzyme GA2ox family member, to be differentially expressed in strong- and weak-dormancy wheat seeds during germination. We confirmed that the ERF transcription factor TaERF-2 A directly bound to the TaGA2ox2-3B promoter and enhanced its transcription. Germination tests indicated that TaERF-2 A positively regulated seed dormancy in wheat. Additionally, 12 mutations were identified within the promoter and coding regions of TaGA2ox2-3B when comparing strong- and weak-dormancy wheat varieties. Six molecular markers were developed to verify correlations between these mutations and seed dormancy. Transgenic experiments verified the potential of the TaGA2ox2-3B+2246-A allele to enhance seed dormancy. Physiological and biochemical analyses indicated that the TaERF-2 A-TaGA2ox2-3B module modulated seed dormancy by influencing GA metabolism and signaling pathways. Collectively, this study revealed the molecular mechanism of GA regulating seed dormancy, and identified genetic resources and molecular markers to breed wheat varieties with preharvest sprouting resistance.

Validation of QTLs for Resistance to Pre-Harvest Sprouting in a Panel of European Wheat Cultivars

Pre-harvest sprouting (PHS) of wheat poses a major challenge to global food security due to its negative impact on grain yield and quality. In the present study, we conducted the validation of previously published markers or functional markers associated with PHS resistance in a panel of 200 wheat cultivars adapted to Southeastern European conditions. In field experiments conducted in four environments in Croatia, the germination index (GI) was assessed, and significant genetic, environmental, and genotype-environment interactions were detected. The broad-sense heritability for GI was high (0.86), confirming the predominant role of genetic factors in determining PHS resistance. Twenty-two polymorphic SNP markers were analyzed for their effects on GI, of which nine markers from chromosomes 3A, 3B, 4A, 5A, and 7B showed significant genotypic effects across environments, especially TaMKK3-A and wsnp_Ex_rep_c66324_64493429. In addition, nine marker combinations were identified, which showed significant differences in GI between allele combinations. Overall, this study elucidates the genetic basis of PHS resistance in wheat cultivars adapted to the agro-climatic conditions of Southeast Europe and provides insights for marker-assisted breeding strategies to improve PHS resistance.

Unraveling Allelic Impacts on Pre-Harvest Sprouting Resistance in TaVP1-B of Chinese Wheat Accessions Using Pan-Genome

The TaVP1-B gene, located on the 3B chromosome of wheat, is a homolog of the Viviparous-1 (VP-1) gene of maize and was reported to confer resistance to pre-harvest sprouting (PHS) in wheat. In this study, the structure of the TaVP1-B gene was analyzed using the wheat pan-genome consisting of 20 released cultivars (19 wheat are from China), and 3 single nucleotide polymorphisms (SNPs), which were identified at the 496 bp, 524 bp, and 1548 bp of the TaVP1-B CDS region, respectively. Haplotypes analysis showed that these SNPs were in complete linkage disequilibrium and that only two haplotypes designated as hap1 (TGG) and hap2 (GAA) were present. Association analysis between TaVP1-B haplotypes and PHS resistance of the 20 wheat cultivars in four experiment environments revealed that the average PHS resistance of accessions with hap1 was significantly better than that of accessions with hap2, which infers the effects of TaVP1-B on wheat PHS resistance. To further investigate the impacts of alleles at the TaVP1-B locus on PHS resistance, the SNP at 1548 bp of the TaVP1-B CDS region was converted to a KASP marker, which was used for genotyping 304 Chinese wheat cultivars, whose PHS resistance was evaluated in three environments. The average sprouting rates (SRs) of 135 wheat cultivars with the hap1 were significantly lower than the 169 cultivars with the hap2, validating the impacts of TaVP1-B on PHS resistance in Chinese wheat. The present study provided the breeding-friendly marker for functional variants in the TaVP1-B gene, which can be used for genetic improvement of PHS resistance in wheat.

Linkage and association analysis to identify wheat pre-harvest sprouting resistance genetic regions and develop KASP markers

Pre-harvest sprouting (PHS) of wheat (Triticum aestivum L.) is one of the complex traits that result in rainfall-dependent reductions in grain production and quality worldwide. Breeding new varieties and germplasm with PHS resistance is of great importance to reduce this problem. However, research on markers and genes related to PHS resistance is limited, especially in marker-assisted selection (MAS) wheat breeding. To this end, we studied PHS resistance in recombinant inbred line (RIL) population and in 171 wheat germplasm accessions in different environments and genotyped using the wheat Infinium 50 K/660 K SNP array. Quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) identified 59 loci controlling PHS. Upon comparison with previously reported QTL affecting PHS, 16 were found to be new QTL, and the remaining 43 loci were co-localized with QTL from previous studies. We also pinpointed 12 candidate genes within these QTL intervals that share functional similarities with genes previously known to influence PHS resistance. In addition, we developed and validated two kompetitive allele-specific PCR (KASP) markers within the chromosome 7B region identified by linkage analysis. These QTL, candidate genes, and the KASP marker identified in this study have the potential to improve PHS resistance of wheat, and they may enhance our understanding of the genetic basis of PHS resistance, thus being useful for MAS breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01526-0.

Utilizing Short Interspersed Nuclear Element as a Genetic Marker for Pre-Harvest Sprouting in Wheat

Pre-harvest sprouting (PHS) is a complex abiotic stress caused by multiple exogenous and endogenous variables that results in random but significant quality and yield loss at the terminal crop stage in more than half of the wheat-producing areas of the world. Systematic research over more than five decades suggests that addressing this challenge requires tools beyond the traditional genetic manipulation approach. Previous molecular studies indicate a possible role of epigenetics in the regulation of seed dormancy and PHS in crops, especially through RNA-directed DNA methylation (RdDM) pathways mediated by Argonaute (AGO) proteins. In this study, we explore the role of the AGO802B gene associated with PHS resistance in wheat, through the presence of a SINE retrotransposon insertion. The current study found the SINE insertion at 3'UTR of the TaAGO802B present in 73.2% of 41 cultivars analyzed and in 92.6% of the resistant cultivar subset. The average expression of TaAGO802B in cultivars with the SINE insertion was 73.3% lower than in cultivars without insertion. This study also indicated a significant positive correlation between the PHS score and methylation levels in the cultivars. The resistant cultivars with the SINE insertion recorded 54.7% lower methylation levels than susceptible cultivars. Further analysis of a DH population (Sadash × P2711) reveals that SINE insertion co-segregates with PHS resistance. This sets forth the SINE insertion in TaAGO802B as a genetic marker for screening wheat germplasm and as an efficient tool for breeding PHS-resistant wheat cultivars.

Mapping of a Major-Effect Quantitative Trait Locus for Seed Dormancy in Wheat

The excavation and utilization of dormancy loci in breeding are effective endeavors for enhancing the resistance to pre-harvest sprouting (PHS) of wheat varieties. CH1539 is a wheat breeding line with high-level seed dormancy. To clarify the dormant loci carried by CH1539 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross of weak dormant SY95-71 and strong dormant CH1539 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2437 SNP markers was constructed. Then, the germination percentage (GP) and germination index (GI) of the seeds from each RIL were estimated. Two QTLs for GP on chromosomes 5A and 6B, and four QTLs for GI on chromosomes 5A, 6B, 6D and 7A were identified. Among them, the QTL on chromosomes 6B controlling both GP and GI, temporarily named QGp/Gi.sxau-6B, is a major QTL for seed dormancy with the maximum phenotypic variance explained of 17.66~34.11%. One PCR-based diagnostic marker Ger6B-3 for QGp/Gi.sxau-6B was developed, and the genetic effect of QGp/Gi.sxau-6B on the RIL population and a set of wheat germplasm comprising 97 accessions was successfully confirmed. QGp/Gi.sxau-6B located in the 28.7~30.9 Mbp physical position is different from all the known dormancy loci on chromosomes 6B, and within the interval, there are 30 high-confidence annotated genes. Our results revealed a novel QTL QGp/Gi.sxau-6B whose CH1539 allele had a strong and broad effect on seed dormancy, which will be useful in further PHS-resistant wheat breeding.

Genome-wide association mapping for pre-harvest sprouting in European winter wheat detects novel resistance QTL, pleiotropic effects, and structural variation in multiple genomes

Pre-harvest sprouting (PHS), germination of seeds before harvest, is a major problem in global wheat (Triticum aestivum L.) production, and leads to reduced bread-making quality in affected grain. Breeding for PHS resistance can prevent losses under adverse conditions. Selecting resistant lines in years lacking pre-harvest rain, requires challenging of plants in the field or in the laboratory or using genetic markers. Despite the availability of a wheat reference and pan-genome, linking markers, genes, allelic, and structural variation, a complete understanding of the mechanisms underlying various sources of PHS resistance is still lacking. Therefore, we challenged a population of European wheat varieties and breeding lines with PHS conditions and phenotyped them for PHS traits, grain quality, phenological and agronomic traits to conduct genome-wide association mapping. Furthermore, we compared these marker-trait associations to previously reported PHS loci and evaluated their usefulness for breeding. We found markers associated with PHS on all chromosomes, with strong evidence for novel quantitative trait locus/loci (QTL) on chromosome 1A and 5B. The QTL on chromosome 1A lacks pleiotropic effect, for the QTL on 5B we detected pleiotropic effects on phenology and grain quality. Multiple peaks on chromosome 4A co-located with the major resistance locus Phs-A1, for which two causal genes, TaPM19 and TaMKK3, have been proposed. Mapping markers and genes to the pan-genome and chromosomal alignments provide evidence for structural variation around this major PHS-resistance locus. Although PHS is controlled by many loci distributed across the wheat genome, Phs-A1 on chromosome 4A seems to be the most effective and widely deployed source of resistance, in European wheat varieties.

Heat Stress-Tolerant Quantitative Trait Loci Identified Using Backcrossed Recombinant Inbred Lines Derived from Intra-Specifically Diverse Aegilops tauschii Accessions

In the face of climate change, bringing more useful alleles and genes from wild relatives of wheat is crucial to develop climate-resilient varieties. We used two populations of backcrossed recombinant inbred lines (BIL1 and BIL2), developed by crossing and backcrossing two intra-specifically diverse Aegilops tauschii accessions from lineage 1 and lineage 2, respectively, with the common wheat cultivar 'Norin 61'. This study aimed to identify quantitative trait loci (QTLs) associated with heat stress (HS) tolerance. The two BILs were evaluated under heat stress environments in Sudan for phenology, plant height (PH), grain yield (GY), biomass (BIO), harvest index (HI), and thousand-kernel weight (TKW). Grain yield was significantly correlated with BIO and TKW under HS; therefore, the stress tolerance index (STI) was calculated for these traits as well as for GY. A total of 16 heat-tolerant lines were identified based on GY and STI-GY. The QTL analysis performed using inclusive composite interval mapping identified a total of 40 QTLs in BIL1 and 153 QTLs in BIL2 across all environments. We detected 39 QTLs associated with GY-STI, BIO-STI, and TKW-STI in both populations (14 in BIL1 and 25 in BIL2). The QTLs associated with STI were detected on chromosomes 1A, 3A, 5A, 2B, 4B, and all the D-subgenomes. We found that QTLs were detected only under HS for GY on chromosome 5A, TKW on 3B and 5B, PH on 3B and 4B, and grain filling duration on 2B. The higher number of QTLs identified in BIL2 for heat stress tolerance suggests the importance of assessing the effects of intraspecific variation of Ae. tauschii in wheat breeding as it could modulate the heat stress responses/adaptation. Our study provides useful genetic resources for uncovering heat-tolerant QTLs for wheat improvement for heat stress environments.

Mining Aegilops tauschii genetic diversity in the background of bread wheat revealed a novel QTL for seed dormancy

Due to the low genetic diversity in the current wheat germplasm, gene mining from wild relatives is essential to develop new wheat cultivars that are more resilient to the changing climate. Aegilops tauschii, the D-genome donor of bread wheat, is a great gene source for wheat breeding; however, identifying suitable genes from Ae. tauschii is challenging due to the different morphology and the wide intra-specific variation within the species. In this study, we developed a platform for the systematic evaluation of Ae. tauschii traits in the background of the hexaploid wheat cultivar 'Norin 61' and thus for the identification of QTLs and genes. To validate our platform, we analyzed the seed dormancy trait that confers resistance to preharvest sprouting. We used a multiple synthetic derivative (MSD) population containing a genetic diversity of 43 Ae. tauschii accessions representing the full range of the species. Our results showed that only nine accessions in the population provided seed dormancy, and KU-2039 from Afghanistan had the highest level of seed dormancy. Therefore, 166 backcross inbred lines (BILs) were developed by crossing the synthetic wheat derived from KU-2039 with 'Norin 61' as the recurrent parent. The QTL mapping revealed one novel QTL, Qsd.alrc.5D, associated with dormancy explaining 41.7% of the phenotypic variation and other five unstable QTLs, two of which have already been reported. The Qsd.alrc.5D, identified for the first time within the natural variation of wheat, would be a valuable contribution to breeding after appropriate validation. The proposed platform that used the MSD population derived from the diverse Ae. tauschii gene pool and recombinant inbred lines proved to be a valuable platform for mining new and important QTLs or alleles, such as the novel seed dormancy QTL identified here. Likewise, such a platform harboring genetic diversity from wheat wild relatives could be a useful source for mining agronomically important traits, especially in the era of climate change and the narrow genetic diversity within the current wheat germplasm.

GWAS and genomic prediction for pre-harvest sprouting tolerance involving sprouting score and two other related traits in spring wheat

In wheat, a genome-wide association study (GWAS) and genomic prediction (GP) analysis were conducted for pre-harvest sprouting (PHS) tolerance and two of its related traits. For this purpose, an association panel of 190 accessions was phenotyped for PHS (using sprouting score), falling number, and grain color over two years and genotyped with 9904 DArTseq based SNP markers. GWAS for main-effect quantitative trait nucleotides (M-QTNs) using three different models (CMLM, SUPER, and FarmCPU) and epistatic QTNs (E-QTNs) using PLINK were performed. A total of 171 M-QTNs (CMLM, 47; SUPER, 70; FarmCPU, 54) for all three traits, and 15 E-QTNs involved in 20 first-order epistatic interactions were identified. Some of the above QTNs overlapped the previously reported QTLs, MTAs, and cloned genes, allowing delineating 26 PHS-responsive genomic regions that spread over 16 wheat chromosomes. As many as 20 definitive and stable QTNs were considered important for use in marker-assisted recurrent selection (MARS). The gene, TaPHS1, for PHS tolerance (PHST) associated with one of the QTNs was also validated using the KASP assay. Some of the M-QTNs were shown to have a key role in the abscisic acid pathway involved in PHST. Genomic prediction accuracies (based on the cross-validation approach) using three different models ranged from 0.41 to 0.55, which are comparable to the results of previous studies. In summary, the results of the present study improved our understanding of the genetic architecture of PHST and its related traits in wheat and provided novel genomic resources for wheat breeding based on MARS and GP.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01357-5.

Identification of a stable major-effect quantitative trait locus for pre-harvest sprouting in common wheat (Triticum aestivum L.) via high-density SNP-based genotyping

A major and stable QTL cQSGR.sau.3D, which can explain 33.25% of the phenotypic variation in SGR, was mapped and validated, and cQSGR.sau.3D was found to be independent of GI. In this study, a recombinant inbred line (RIL) population containing 304 lines derived from the cross of Chuan-nong17 (CN17) and Chuan-nong11 (CN11) was genotyped using the Wheat55K single-nucleotide polymorphism array. A high-density genetic map consisting of 8329 markers spanning 4131.54 cM and distributed across 21 wheat chromosomes was constructed. QTLs for whole spike germination rate (SGR) were identified in multiple years. Six and fourteen QTLs were identified using the Inclusive Composite Interval Mapping-Biparental Populations and Multi-Environment Trial methods, respectively. A total of 106 digenic epistatic QTLs were also detected in this study. One of the additive QTLs, cQSGR.sau.3D, which was mapped in the region from 3.5 to 4.5 cM from linkage group 3D-2 on chromosome 3D, can explain 33.25% of the phenotypic variation in SGR and be considered a major and stable QTL for SGR. This QTL was independent of the seeds' germination traits, such as germination index. One Kompetitive Allele-Specific PCR (KASP) marker, KASP-AX-110772653, which is tightly linked to cQSGR.sau.3D, was developed. The genetic effect of cQSGR.sau.3D on SGR in the RIL and natural populations was successfully confirmed. Furthermore, within the interval in which cQSGR.sau.3D is located in Chinese Spring reference genomes, thirty-seven genes were found. cQSGR.sau.3D may provide new resources for pre-harvest sprouting resistance breeding of wheat in the future.

Crop traits enabling yield gains under more frequent extreme climatic events

Climate change (CC) in central China will change seasonal patterns of agricultural production through increasingly frequent extreme climatic events (ECEs). Breeding climate-resilient wheat (Triticum aestivum L.) genotypes may mitigate adverse effects of ECEs on crop productivity. To reveal crop traits conducive to long-term yield improvement in the target population of environments, we created 8,192 virtual genotypes with contrasting but realistic ranges of phenology, productivity and waterlogging tolerance. Using these virtual genotypes, we conducted a genotype (G) by environment (E) by management (M) factorial analysis (G×E×M) using locations distributed across the entire cereal cropping zone in mid-China. The G×E×M invoked locally-specific sowing dates under future climates that were premised on shared socioeconomic pathways SSP5-8.5, with a time horizon centred on 2080. Across the simulated adaptation landscape, productivity was primarily driven by yield components and phenology (average grain yield increase of 6-69% across sites with optimal combinations of these traits). When incident solar radiation was not limiting carbon assimilation, ideotypes with higher grain yields were characterised by earlier flowering, higher radiation-use efficiency and larger maximum kernel size. At sites with limited solar radiation, crops required longer growing periods to realise genetic yield potential, although higher radiation-use efficiency and larger maximum kernel size were again prospective traits enabling higher rates of yield gains. By 2080, extreme waterlogging stress in some regions of mid-China will impact substantially on productivity, with yield penalties of up to 1,010 kg ha^-1. Ideotypes with optimal G×M could mitigate yield penalty caused by waterlogging by up to 15% under future climates. These results help distil promising crop trait by best management practice combinations that enable higher yields and robust adaptation to future climates and more frequent extreme climatic events, including flash flooding and soil waterlogging.

Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays

Preharvest sprouting (PHS) significantly reduces grain yield and quality. Identification of genetic loci for PHS resistance will facilitate breeding sprouting-resistant wheat cultivars. In this study, we constructed a genetic map comprising 1,702 non-redundant markers in a recombinant inbred line (RIL) population derived from cross Yangxiaomai/Zhongyou9507 using the wheat 15K single-nucleotide polymorphism (SNP) assay. Four quantitative trait loci (QTL) for germination index (GI), a major indicator of PHS, were identified, explaining 4.6-18.5% of the phenotypic variances. Resistance alleles of Qphs.caas-3AL, Qphs.caas-3DL, and Qphs.caas-7BL were from Yangxiaomai, and Zhongyou9507 contributed a resistance allele in Qphs.caas-4AL. No epistatic effects were detected among the QTL, and combined resistance alleles significantly increased PHS resistance. Sequencing and linkage mapping showed that Qphs.caas-3AL and Qphs.caas-3DL corresponded to grain color genes Tamyb10-A and Tamyb10-D, respectively, whereas Qphs.caas-4AL and Qphs.caas-7BL were probably new QTL for PHS. We further developed cost-effective, high-throughput kompetitive allele-specific PCR (KASP) markers tightly linked to Qphs.caas-4AL and Qphs.caas-7BL and validated their association with GI in a test panel of cultivars. The resistance alleles at the Qphs.caas-4AL and Qphs.caas-7BL loci were present in 72.2 and 16.5% cultivars, respectively, suggesting that the former might be subjected to positive selection in wheat breeding. The findings provide not only genetic resources for PHS resistance but also breeding tools for marker-assisted selection.

The Inheritable Characteristics of Monoecy and Parthenogenesis Provide A Means for Establishing A Doubled Haploid Population in the Economically Important Brown Alga Undaria pinnatifida (Laminariales, Alariaceae)

Monoecy and parthenogenesis exist in certain male and female gametophytes of the brown alga Undaria pinnatifida. The inheritance of these traits is not known. In this study, we made a cross between a male and a female gametophyte clone which could exhibit monoecy and parthenogenesis phenotypes, respectively, and obtained their next-generation gametophyte offspring. We found that under conditions suitable for gametogenesis, all of the male offspring (n = 100) exhibited monoecy phenotype and all of the female offspring (n = 100) only formed oogonia and underwent parthenogenesis, suggesting that monoecy and parthenogenesis phenotypes are inheritable. Then, we established a doubled haploid (DH) population through monoecious selfing and parthenogenesis, and evaluated the young sporophyte growth and the maximum quantum yield (Fv /Fm ) of 10 "male" and 10 "female" DH lines. On day 60, the average length of the "male" DH lines was significantly larger than that of the "female" DH lines, while their average Fv /Fm values were not significantly different. Monoecious selfing seemed superior to parthenogenesis as the sporophyte formation efficiency, and the young sporophyte growth was better in the former than in the latter. We also crossed two monoecious gametophytes with another male gametophyte, and a parentage analysis showed success of obtaining hybrid sporophytes, indicating that the female gametes released by the monoecious gametophyte can actually be fertilized by sperm. The approach of establishing a DH population proposed here will be useful in genetic breeding and quantitative trait loci mapping in U. pinnatifida and may be applicable to other kelp species.