Theoretical and Applied Genetics最新文献

Verticillium wilt (VW), caused by the soil-borne fungus Verticillium dahliae, stands as one of the most destructive diseases affecting cotton production world-wide. Developing and deploying VW-resistant cotton varieties represents the most effective and sustainable strategy for mitigating the impact of VW. However, breeding VW-resistant upland cotton (Gossypium hirsutum, Gh) varieties is constrained by the limited VW resistance in Gh. One strategy for improving VW resistance of Gh varieties is to introgress resistance alleles from sea-island cotton (Gossypium barbadense, Gb). Interspecific chromosome segment substitution lines (CSSLs) developed based on Gh x Gb offer materials not only for breeding VW-resistant Gh varieties but also for mapping and cloning VW resistance genes. In this study, we used 318 CSSLs derived from Emian-22 (Gh) × 3-79 (Gb) for mapping of VW-resistant QTLs based on phenotypic data collected from 3 years of field disease-nursery based experiments and 1.3 million single nucleotide polymorphisms identified among the CSSLs. A genome-wide association study revealed 77 VW resistance QTLs, with only 12 of them overlapping with known VW resistance loci, suggesting that the CSSL population is a valuable resource for mining novel VW-resistant alleles. In the two VW-resistant QTLs on chromosomes A01 and D12, nonsynonymous mutations were found in several annotated genes related to biotic stress responses. Ghi_D12G018010 (GhHIR1) in the D12 locus was shown to positively contribute to VW resistance, as down-regulating the gene by virus-induced gene silencing led to reduction of VW resistance. The findings of this study provide candidate genes and markers for improving cotton VW resistance through molecular breeding.

Ability to accurately predict multiple growth-related traits over plant developmental trajectories has the potential to revolutionize crop breeding and precision agriculture. Despite increased availability of time-resolved data for multiple traits from high-throughput phenotyping platforms of model plants and crops, genomic prediction is largely applied independently to a small number of traits, often neglecting their dynamics. Here, we compared and contrasted the performance of MegaLMM and dynamicGP as well as hybrid variants, using MegaLMM in place of RR-BLUP for component matrix prediction, which can handle high-dimensional temporal data for multi-trait genomic prediction. The comparative analysis made use of time series for 50 geometric, color, and texture traits in a maize multi-parent advanced generation inter-cross (MAGIC) population. The performance of the approaches was assessed using snapshot and longitudinal accuracy, quantified as the Pearson correlation (PCC) and mean squared error (MSE), thereby providing insight into the ability to predict multiple traits at a single time point or the dynamics of individual traits over the considered time domain, respectively. We found that MegaLMM outperforms dynamicGP in terms of both snapshot and longitudinal PCC over an observed time interval, but not in terms of snapshot MSE. We also analyzed the characteristics of trait developmental trajectories associated with predictive performance. This study goes further to demonstrate that dynamicGP is the only time-dependent genomic prediction approach which can forecast multiple traits beyond the set of training time points and paves the way for careful investigation of factors that affect the capacity to predict dynamics of multiple traits from genetic markers alone.

Seed dormancy is essential to avoid pre-harvest sprouting (PHS), and germination is vital for agricultural production planning and malting. The malting barley genetic resource Chikukei 9713 is PHS tolerant but quickly breaks seed dormancy after harvest. We found that Chikukei 9713 and the barley cultivar Seijo 17 were PHS tolerant because exon-9 of the seed dormancy gene sd1 was of the dormant type. However, the rapidity of breaking seed dormancy depended on the threshing method. Both varieties germinated slowly after hand threshing, whereas Chikukei 9713, but not Seijo 17, germinated quickly after machine threshing. Using the 94 F₂ individuals and 94 F₃ lines populations derived from a cross between Chikukei 9713 and Seijo 17, we found a genetic region that controlled the effect of the threshing method on breaking seed dormancy (named bsd1) located on the short arm of chromosome 2H (23.4-24.9 Mbp) with GRAS-Di (Genotyping by Random Amplicon Sequencing-Direct) and CAPS markers. Further analysis revealed that bsd1 had a maximum LOD score of 21.4 and explained 65% of the variance. Our findings regarding this novel gene are an important genetic resource for stable malting barley production and sowing planning. Utilizing bsd1 and other seed dormancy genes will enable breeding of PHS-resistant barley cultivars that germinate quickly after machine harvesting.

Drought is the primary factor contributing to crop yield loss. Therefore, enhancing the drought tolerance of foxtail millet, a globally significant food crop, is essential for ensuring global food security. We analyzed 425 foxtail millet samples from the Xinjiang Academy of Agricultural Sciences using 1,304,248 highly polymorphic SNPs for a genome-wide association study, and a total of 77 QTL regions were detected across three environments. Linkage disequilibrium (LD) analysis, population genetic structure analysis, K-means clustering, and phylogenetic tree construction revealed that foxtail millet in different subgroups exhibited certain regional differences. The secondary screening of QTL region genes combined with transcriptome analysis identified six genes with significant expression differences. These drought-responsive genes in foxtail millet function as protein kinases, glycosyltransferases, CTP synthetases, and transcription factors. Haplotype analysis identified 8 phenotypically distinct haplotypes in candidate genes associated with drought stress. Expression levels of genes associated with drought tolerance and yield, validated by RT-qPCR, were largely consistent with transcriptome analysis results. This study's results offer a scientifically significant reference for genetic research and improvement in foxtail millet yield under drought stress.

One-third of paddy soils are globally deficient in zinc (Zn) and 40% of Zn loss in the procession from brown rice to polished rice, which results in the global issue of hidden hunger, e.g., the micronutrient deficiencies in the rice-based population of developing countries. In the recent decades, biofortification of cereal food crops with Zn has emerged as a promising solution. Herein, we comprehensively reviewed the entire process of Zn in paddy soil to human diet, including the regulatory mechanism underlying Zn absorption, transport, distribution, and accumulation in rice grain. Moreover, biofortification approaches of Zn have been summarized in conventional breeding, genetic engineering, agronomic management, and seed priming. Meanwhile, entire process and key nodes from paddy soil to human diet consumption were highlighted. Finally, future directions and challenges of Zn biofortification in rice were proposed. These comprehensive results show the great promise for addressing Zn deficiency and promoting the human nutrition.

Key message: Six highly alkali-tolerant wheat germplasms were identified, 206 MTAs related to germination traits and 198 significant PC-MTAs were detected, and 2 KASP markers for resistance breeding were developed. Soil alkalization is a major constraint on global wheat production, making it essential to uncover the genetic mechanisms underlying alkali tolerance during germination. Here, a genome-wide association study (GWAS) was conducted on 314 wheat accessions evaluated under 0.15% Na₂CO₃ stress and control conditions. Phenotypic screening showed a strong suppression of seedling biomass and root growth under alkalinity stress, while germination rate remained largely unaffected. Based on principal component analysis, the accessions were classified into five tolerance groups: six highly tolerant, 57 tolerant, 92 moderate, 110 sensitive, and 35 highly sensitive. GWAS identified 206 significant marker-trait associations (MTAs) for nine germination-related traits, with five loci (MTA25, MTA29, MTA80, MTA129, and MTA166) consistently detected across both conditions. Allelic effect and candidate gene analyses were performed for three of these stable loci (MTA25, MTA29, and MTA80). Principal component analysis-integrated GWAS detected an additional 198 significant MTAs, 51 of which co-localized with phenotype-based MTAs and were validated as core stress-responsive loci. In addition, Kompetitive Allele Specific PCR markers associated with sheath length and germination percentage were developed. These findings enhance our understanding of the genetic basis of alkali tolerance during wheat germination and provide valuable molecular resources for breeding alkali-tolerant wheat varieties.

Key message: Mutations in TaPRR59 impact transcript levels of some key flowering genes and show earlier heading time and reduced plant height. Favorable haplotype TaPRR59-A1-Hapla was positively selected in wheat breeding programs. The circadian clock system is a crucial endogenous rhythmic regulatory mechanism with a significant role in plant growth and development. The pseudo-response regulator (PRR) family is a pivotal component of circadian networks. In the present study, we cloned the wheat PRR family member TaPRR59 and investigated its function using gene editing, transcriptome sequencing, haplotype analysis, and association analysis. The expression profile of TaPRR59 over a 24-h period exhibited a diurnal rhythmic expression pattern. Luciferase transient transcriptional assay demonstrated that TaPRR59 acts as a transcriptional repressor in the nucleus. The taprr59-ABD-KO gene-edited lines produced using the CRISPR/Cas9 genome-editing system had earlier heading time and reduced plant height. Overexpression of TaPRR59-D1 in rice significantly delayed the heading date, reduced plant height and thousand-grain weight, and increased the number of grains per panicle. Transcriptome analysis revealed the transcript levels of several key flowering genes and chlorophyll a-b binding protein-related genes were up- or down-regulated in the taprr59 mutant plants. Association analysis showed that natural variations at TaPRR59-A1, TaPRR59-B1, and TaPRR59-D1 were significantly associated with yield traits such as plant height, thousand-grain weight, and heading date. Geographical analysis showed distinctive distribution characteristics of TaPRR59 haplotypes in different agroecological production zones. Additionally, the significant difference in frequency of the favorable haplotype TaPRR59-A1-Hapla between landraces and modern cultivars indicates that it has been subject to directional selection during wheat breeding. This research provided novel insights into the influence of the circadian clock system on agronomic traits and provided useful molecular markers and genetic resources for wheat breeding.

Rice yield-related traits are regulated by numerous quantitative trait loci (QTLs). Pyramiding these QTLs offers a promising strategy for crop yield improvement; however, this approach is constrained by the limited understanding of the interactions among these QTLs. In this study, we demonstrated that the QTL DTH8 significantly increases branch numbers, panicle length, and number of total grains per panicle in rice. Notably, the DTH8⁹³¹¹ allele exhibited a more pronounced effect on enhancing yield-related traits compared to DTH8^Nip. Furthermore, QTL pyramiding involving SD1 and DTH8 indicated that the regulation of panicle architecture by DTH8 partially depends on SD1. Genetic analysis revealed an interaction between these two QTL/genes with respect to panicle-related traits. Dual-luciferase and ChIP-PCR analyses suggested that DTH8 might regulate the expression of SD1, thereby governing branch numbers, panicle length, and number of total grains per panicle. Additionally, our findings highlight the importance of avoiding the simultaneous pyramiding of sd1 and DTH8⁹³¹¹ in practical breeding programs due to their genetic and molecular interactions.

Key message: Allelic variation in Ym2 is available for breeding WYMV resistant bread wheat in China. Infection by Wheat yellow mosaic virus reduces both the yield and end-use quality of winter wheat. As the pathogen resides in the soil, the most effective disease control strategy is to breed varieties harboring a gene or genes conferring resistance. One such gene is Ym2, which has been introduced into bread wheat from its diploid wild relative Aegilops sharonensis. The gene has since been isolated and shown to encode a CC-NBS-LRR protein, but no concerted attempt has been made to date to characterize whether allelic variants of the gene are present in the bread wheat gene pool. In conjunction with previously published sequence data, the newly acquired data have enabled the identification of a total of 22 haplotypes at Ym2 locus, of which 14 are functional with respect to conferring resistance to WYMV; of these 14, 12 encode a non-synonymous amino acid variant(s), while two feature the insertion of a short nucleotide sequence into the coding region. While the functional haplotypes are all represented among the American and Japanese entries, none were harbored by Chinese germplasm, indicating that Ym2 has not been exploited to date by Chinese wheat breeders.

Drought stress is a major global challenge in crop production. The occurrence of drought during seed germination directly affects crop establishment and final yield. In this work, we performed whole-genome resequencing of 414 mungbean (Vigna radiata (L.) R. Wilczek) germplasms and identified 4,875,142 high-quality single-nucleotide polymorphisms (SNPs). Two seed germination traits of the mungbean panel under drought stress across two environments were evaluated via a genome-wide association study (GWAS), and the results revealed a significant quantitative trait locus (QTL). Additionally, kompetitive allele-specific PCR (KASP) markers that can identify the germination characteristics of mungbean seeds under drought stress were developed and verified. Moreover, among the nine candidate genes near this site, the expression levels of different haplotypes of VrERF088 differed. Interestingly, the only ABA-responsive element in the VrERF088 promoter was mutated. The results demonstrated that VrABI5 activates the transcriptional activity of the Hap1 promoter by binding to the ABRE motif. The overexpression of VrERF088 in Arabidopsis thaliana significantly reduced the germination rate of plants under drought stress by increasing the expression of the ABA response genes AtPM6 and AtLEA4 and reducing the expression of the germination-related genes AtEXPAs, resulting in hypersensitivity to ABA. Our results indicate that mutation of the ABRE motif in the VrERF088 promoter results in a relatively high germination rate under drought stress.