Theoretical and Applied Genetics最新文献

Wheat (Triticum aestivum L.) is one of the most important cereal crops, with its grain serving as a predominant staple food source on a global scale. However, there are many biotic and abiotic stresses challenging the stability of wheat production. Among the abiotic stresses, drought is recognized as a significant stress and poses a substantial threat to food production and quality throughout the world. Raising drought tolerance of wheat varieties through genetic regulation is therefore considered as one of the most effective ways to combat the challenges caused by drought stress. Meta-QTL analysis has demonstrated its effectiveness in identifying consensus QTL regions in wheat drought resistance in numerous instances. In this study, we present a comprehensive meta-analysis aimed at unraveling the drought tolerance genetic basis associated with agronomic traits in bread wheat. Extracting data from 34 previously published studies, we aggregated a corpus of 1291 Quantitative Trait Loci (QTL) pertinent to wheat drought tolerance. Then, the translation of the consensus genetic map yielded a comprehensive compendium of 49 distinct MQTLs, each associated with diverse agronomic traits. Prominently featured among the MQTLs were MQTLs 1.1, 1.7, 1.8 (1D), 4.1 (4A), 4.6 (4D), 5.2 (5B), 6.6 (6B), and 7.2 (7B), distinguished as pivotal MQTLs offering significant potential for application in marker-assisted breeding endeavors. Altogether, a total of 66 putative candidate genes (CGs)-related drought tolerance were identified. This work illustrates a translational research approach in transferring information from published mapping studies to genomic regions hosting major QTLs governing key agronomical traits in wheat.

Key message: Total 60-QRC for FLM traits were detected by meta-genomics analysis, nine major and stable QTL identified by DH population and validated, and a novel QTL  Qflw.sxau-6BL was fine mapped. The flag leaf is an "ideotypic" morphological trait providing photosynthetic assimilates in wheat. Although flag leaf morphology (FLM) traits had been extensively investigated through genetic mapping, there is a desire for FLM-related loci to be validated in multi-environments and fine mapping. In order to identify the stable genomic regions for FLM traits, we conducted a meta-genomic analysis based on reports from 2008 to 2024. Experimentally, a doubled haploid (DH) population was used to assess the genetic regions associated with FLM traits in nine environments. The meta-genomic analysis extracted 60 QTL-rich clusters (QRC), 45 of which were verified in marker-trait association (MTA) study. Nine major and stable QTL were found being associated with FLM traits across three-to-seven environments including BLUP, with phenotypic variance explained (PVE) ranging from 5.05 to 34.95%. The KASP markers of the nine QTL were validated (P < 0.005) in more than three environments using a panel of diverse wheat collections from Shanxi Province in China. Two co-located major and stable QTL viz. Qflw.sxau-6B.5 and Qfla.sxau-6B.4 were found novel and contributed to increase FLW by 12.09-19.21% and FLA by 5.45-13.28%. They also demonstrated high recombination rates in LD analysis based on the resequencing of 145 wheat landmark cultivars. The fine mapping of Qflw.sxau-6BL narrowed it down to a 1.27 Mb region as a result of the combined genotypic and phenotypic analysis for secondary mapping population. Comparing to NIL-ND3338, the NIL-LF5064 showed higher FLW by 20.45-27.37%, thousand-grain weight by 1.88-2.57% and grain length by 0.47-2.30% across all environments. The expression analysis of 11 tissues revealed seven highly expressed genes within the fine map region. This study provides a genetic basis for the FLM traits for further map-based cloning of FLW genes in wheat.

Key message: A major locus Qfcr.cau-1B conferring resistance to Fusarium crown rot was identified and validated. The putative gene underlying this locus was pinpointed via virus-induced gene silencing. Fusarium crown rot (FCR), caused by various Fusarium pathogens such as Fusarium pseudograminearum and F. culmorum, is a severe soil-borne disease which significantly affected wheat (Triticum aestivum) production in many arid and semi-arid cropping regions of the world. In this study, a total of 5 QTLs associated with FCR resistance were detected on chromosomes 1B, 2B, 3A, 5A, and 7D using a population of 120 F₈ recombinant inbred lines (RIL) derived from a cross between two Chinese germplasm 20828 and SY95-71. A major locus Qfcr.cau-1B, which accounted for up to 28.33% of the phenotypic variation with a LOD value of 10.99, was consistently detected across all three trials conducted. The effect of Qfcr.cau-1B on FCR resistance was further validated using a F₅ RIL population between 20828 and BLS2. Integrated transcriptome and sequence variation analysis showed that three genes including TraesCS1B02G017700, TraesCS1B02G016400, and TraesCS1B02G022300 were potential candidate genes for Qfcr.cau-1B. Of these three genes, the virus-induced silencing of TraesCS1B02G022300 significantly promoted FCR severity, indicating its positive role in FCR resistance. Taken together, results from this study expand our understanding on genetic basis of FCR resistance in wheat and will be indicative for cloning genes conferring FCR resistance.

Key message: The tomato Ty-6 gene conferring resistance against begomoviruses has been cloned and shown to be a variant of DNA polymerase delta subunit 1. Ty-6 is a major resistance gene of tomato that provides resistance against monopartite and bipartite begomoviruses. The locus was previously mapped on chromosome 10, and in this study, we fine-mapped Ty-6 to a region of 47 kb, including four annotated candidate genes. Via whole-genome resequencing of Ty-6 breeding lines and several susceptible breeding lines, the polymorphisms in gene sequences were discovered and gene-associated markers were developed for marker-assistant breeding. Further, virus-induced gene silencing and candidate gene overexpressing in susceptible tomatoes revealed that Ty-6-mediated resistance is controlled by Solyc10g081250, encoding the DNA polymerase delta subunit 1, SlPOLD1. The single nucleotide polymorphism of Ty-6 results in an amino acid change that might influence the fidelity of virus DNA replication.

Key message: The single recessive Chilli veinal mottle virus resistance locus, cvr4, was fine-mapped in pepper through bulked segregant RNA sequencing combined with gene silencing analysis. Chilli veinal mottle virus (ChiVMV) is a widespread pathogen affecting the production of peppers (Capsicum annuum L.) in Asia and Africa. Few loci conferring resistance to ChiVMV have been identified, severely limiting the development of resistant cultivars. To identify ChiVMV resistance genes, we constructed an F_2:3 segregating population derived from a cross between the ChiVMV-resistant cultivar 'CV9' and the susceptible cultivar 'Jeju'. The inheritance study of F_2:3 populations showed a 1:3 ratio of resistant to susceptible individuals, demonstrating the existence of a single recessive ChiVMV resistance gene in CV9; we named this gene cvr4. To map the cvr4 locus, we employed bulked segregant analysis by RNA sequencing (BSR-seq) of pools from resistant and susceptible F_2:3 individuals. We mapped cvr4 to the telomeric region of pepper chromosome 11. To narrow down the cvr4 locus, we developed additional molecular markers in the cvr4 target region, leading to a 2-Mb region of chromosome 11 showing complete co-segregation with the ChiVMV resistance phenotype. Using the polymorphisms identified during BSR-seq, we defined a list of 15 candidate genes for cvr4, which we tested through virus-induced gene silencing analysis for ChiVMV resistance. Of these, the silencing of several genes (DEM.v1.00021323, DEM.v1.00021336, and DEM.v1.00021337) restricted virus spread. Although DEM.v1.00021323 transcript levels were similar between the resistant and susceptible bulks, its alternative spliced isoforms differed in abundance, suggesting that the splicing variants of DEM.v1.00021323 might affect viral infection. These findings may facilitate the breeding of ChiVMV-resistant cultivars in pepper.

Key message: 112 candidate quantitative trait loci (QTLs) and 53 key candidate genes have been identified as associated with stomatal traits in wheat. These include bHLH, MADS-box transcription factors, and mitogen-activated protein kinases (MAPKs). Stomata is a common feature of the leaf surface of plants and serve as vital conduits for the exchange of gases (primarily CO₂ and water vapor) between plants and the external environment. In this study, a comprehensive genome analysis was conducted by integrating genome-wide association study (GWAS) and genome prediction to identify the genomic regions and candidate genes of stomatal traits associated with drought resistance and water-saving properties in a panel of 184 diverse bread wheat genotypes. There were significant variations on stomatal traits in the wheat panel across different environmental conditions. GWAS was conducted with the genotypic data from the wheat 660 K single-nucleotide polymorphism (SNP) chip, and the stomatal traits conducted across three environments during two growing seasons. The final GWAS identified 112 candidate QTLs that exhibited at least two significant marker-trait associations. Subsequent analysis identified 53 key candidate genes, including 13 bHLH transcription factor, 2 MADS-box transcription factors, and 4 mitogen-activated protein kinase genes, which may be strongly associated with stomatal traits. The application of Bayesian ridge regression for genomic prediction yielded an accuracy rate exceeding 60% for all four stomatal traits in both SNP matrices, with stomatal width achieving a rate in excess of 70%. Additionally, three Kompetitive allele-specific PCR markers were developed and validated, representing a significant advancement in marker-assisted prediction. Overall, these results will contribute to a more comprehensive understanding of wheat stomatal traits and provide a valuable reference for germplasm screening and innovation in wheat germplasm with novel stomatal traits.

Key message: Two dwarf bunt resistance QTLs were mapped to chromosome 6D, and KASP markers associated with the loci were developed and validated in a panel of regionally adapted winter wheats. UI Silver is an invaluable adapted resistant cultivar possessing the two identified QTL potentially associated with genes Bt9 and Bt10 and will be useful in future cultivar development to improve dwarf bunt resistance. Dwarf bunt, caused by Tilletia controversa, is a fungal disease of wheat that can cause complete loss of grain yield and quality during epidemics. Traditional breeding for dwarf bunt resistance requires many years of field screening under stringent conditions with disease assessment possible only near or after plant maturity. Molecular marker-assisted selection (MAS) offers a more efficient alternative. This study identified quantitative trait loci (QTL) and associated molecular markers for dwarf bunt resistance in wheat. A doubled haploid (DH) mapping population of 135 lines, derived from bunt-resistant cultivar 'UI Silver' and susceptible line 'Shaan89150', was evaluated in field nursery in Logan, Utah in 2017, 2018, and 2023. The population was genotyped using Illumina 90 K SNP iSelect marker platform. Using inclusive composite interval mapping (ICIM), the major QTL Qdb.ssdhui-6DL was consistently identified on chromosome arm 6DL across all environments, explaining phenotypic variations ranging from 15.29% to 35.40%. Another QTL, Qdb.ssdhui-6DS, was detected on chromosome arm 6DS, explaining approximately 11% of the phenotypic variation. These two QTLs exhibit additive-by-additive effects for increased resistance within the DH population. Kompetitive allele-specific PCR (KASP) markers were developed within QTL intervals and used in a validation panel of regionally adapted winter wheat lines to confirm the association between the two QTL and dwarf bunt resistance. Thus, 'UI Silver' and additional resistant cultivars with these two QTLs are valuable parental lines for improving dwarf bunt resistance through marker-assisted selection. These genetic resources are essential for understanding gene function via map-based gene cloning.

Key message: A major locus SC9.1 was identified and finely mapped into a 92.68 Kb region, and longmi004412 was identified as the casual gene regulating brown seed color in broomcorn millet. Broomcorn millet is a cereal crop with abundant genetic variations in morphology, agronomy, and yield-related traits. The diversity of seed color is among the most distinctive morphological characteristics. However, genetic determinants governing seed coloration have rarely been reported. Here, the F₂ and F₃ populations from a cross between Longmi12 and Zhang778 were employed to elucidate the genetic basis of seed color. Statistical analysis conducted on the seed color in F₁, F_2, and F₃ progeny conclusively demonstrated that brown seed color was controlled by a single dominant locus in broomcorn millet. The genetic control locus, SC9.1, was preliminarily located on chromosome 9 in the 32,175,878-44,281,406 bp region through bulked segregant analysis sequencing (BSA-seq). Furthermore, SC9.1 was narrowed down to a 92.68 kb interval harboring 11 genes using fine mapping with 260 recessive individual genotypes. Combined with gene structural variation, the transcriptome profile, and functional comparison, longmi004412 was identified as the causal gene resulting in brown seed color formation in broomcorn millet. In addition, haplotype analysis of the longmi004412 gene in 516 accessions was performed to clarify the types for broomcorn millet seed color. These findings lay the foundation for precise identification of germplasm at the molecular level, molecular-assisted selection breeding, and the application of gene editing technology in broomcorn millet.

Key message: Unraveling key ABA pathways, including OsWRKY71-OsABA8ox1 and OsbZIP73-OsNCED5, provides valuable insights for improving cold tolerance in rice breeding for cold-prone regions. Cold stress limits rice (Oryza sativa L.) production in cooler climates. This study uncovers how abscisic acid (ABA) signaling enhances cold tolerance in the rice variety Zhonghua 11 (ZH11) compared to the cold-sensitive Kasalath. Under cold stress, ZH11 rapidly accumulates ABA through efficient regulation of key genes. The transcription factor OsWRKY71^ZH11 represses the ABA catabolism gene OsABA8ox1 during early stress, enabling quick ABA accumulation. Additionally, OsbZIP73 regulates the ABA synthesis gene OsNCED5 to maintain ABA balance during prolonged stress. Transgenic ZH11 plants overexpressing OsWRKY71^ZH11 exhibited enhanced cold tolerance, while overexpression of OsWRKY71^Ka did not confer benefits. Haplotype analysis linked allelic variations in OsWRKY71 and OsNCED5 to differences in cold tolerance. Our findings highlight critical ABA signaling pathways that enhance cold tolerance in rice. Targeting these pathways offers promising strategies for breeding cold-resistant rice varieties, improving resilience in cold-prone regions.

Key message: Integrated genome-wide association study and linkage mapping revealed genetic basis of alkalinity tolerance during rice germination. The key gene OsWRKY49 was further verified in transgenic plants. With the widespread use of the rice direct seeding cultivation model, improving the tolerance of rice varieties to salinity-alkalinity at the germination stage has become increasingly important. However, as previous studies have concentrated on neutral salt stress, understanding of alkalinity tolerance is still in its infancy, and the genetic resource data is scarce. Here, we used a natural population composed of 295 japonica rice varieties and a recombinant inbred population including 189 lines derived from Caidao (alkali-sensitive) and WD20342 (alkali-tolerant) to uncover the genetic structure of alkalinity tolerance during rice germination. A total of 15 lead SNPs and six QTLs related to relative germination potential (RGP) and relative germination index (RGI) were detected by genome-wide association study and linkage mapping. Of which, Chr5_28094966, a lead SNP was located in the interval of the mapped major QTL qAT5, that was significantly associated with both RGP and RGI in the two populations. According to the LD block analysis and QTL interval, a 425 kb overlapped region was obtained for screening the candidate genes. After haplotype analysis, qRT-PCR and parental sequence analysis, LOC_Os05g49100 (OsWRKY49) was initially considered as the candidate gene. Having studied the characteristics of rice lines with OsWRKY49 knockout and overexpression, we established that OsWRKY49 could be a positive regulator of alkalinity tolerance in rice at the germination stage. Subcellular localization showed that green fluorescent protein-tagged OsWRKY49 was localized in the nucleus. The application of OsWRKY49 could be useful for increasing alkalinity tolerance of rice direct seeding.