Molecular Breeding最新文献

Seed size is an economically important trait that directly determines the seed yield in soybean. In the current investigation, we used an integrated strategy of linkage mapping, association mapping, haplotype analysis and candidate gene analysis to determine the genetic makeup of four seed size-related traits viz., 100-seed weight (HSW), seed area (SA), seed length (SL), and seed width (SW) in soybean. Linkage mapping identified a total of 23 quantitative trait loci (QTL) associated with four seed size-related traits in the F₂ population; among them, 17 were detected as novel QTLs, whereas the remaining six viz., qHSW3-1, qHSW4-1, qHSW18-1, qHSW19-1, qSL4-1 and qSW6-1 have been previously identified. Six out of 23 QTLs were major possessing phenotypic variation explained (PVE) ≥ 10%. Besides, the four QTL Clusters/QTL Hotspots harboring multiple QTLs for different seed size-related traits were identified on Chr.04, Chr.16, Chr.19 and Chr.20. Genome-wide association study (GWAS) identified a total of 62 SNPs significantly associated with the four seed size-related traits. Interestingly, the QTL viz., qHSW18-1 was identified by both linkage mapping and GWAS, and was regarded as the most stable loci regulating HSW in soybean. In-silico, sequencing and qRT-PCR analysis identified the Glyma.18G242400 as the most potential candidate gene underlying the qHSW18-1 for regulating HSW. Moreover, three haplotype blocks viz., Hap2, Hap6A and Hap6B were identified for the SW trait, and one haplotype was identified within the Glyma.18G242400 for the HSW. These four haplotypes harbor three to seven haplotype alleles across the association mapping panel of 350 soybean accessions, regulating the seed size from lowest to highest through intermediate phenotypes. Hence, the outcome of the current investigation can be utilized as a potential genetic and genomic resource for breeding the improved seed size in soybean.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01525-1.

Brassica napus, a globally significant oilseed crop, exhibits a wide distribution across diverse climatic zones. B. napus is being increasingly susceptible to distinct diseases, such as blackleg, clubroot and sclerotinia stem rot, leading to substantial reductions in yield. Nucleotide-binding site leucine-rich repeat genes (NLRs), the most pivotal family of resistance genes, can be effectively harnessed by identifying and uncovering their diversity to acquire premium disease-resistant gene resources. Here, we collected the genomes of 23 accessions and established the first comprehensive pan-NLRome in B. napus by leveraging multiple genomic resources. We observe significant variation in the number of NLR genes across different B. napus accessions, ranging from 189 to 474. Notably, TNL (TIR-NBS-LRR) genes constitute approximately half of the total count, indicating their predominant presence in B. napus. The number of NLRs in the C subgenome is significantly higher than that in the A subgenome, and chromosome C09 exhibits the highest density of NLR genes with featuring multiple NLR clusters. Domain analysis reveals that the integrated domains significantly enhance the diversity of NLRs, with B3 DNA binding, VQ, and zinc fingers being the most prevalent integrated domains. Pan-genomic analysis reveals that the core type of NLR genes, which is present in most accessions, constitutes approximately 58% of the total NLRs. Furthermore, we conduct a comparative analysis of the diversity of NLR genes across distinct ecotypes, leading to the identification of ecotype-specific NLRs and their integrated domains. In conclusion, our study effectively addresses the limitations of a single reference genome and provides valuable insights into the diversity of NLR genes in B. napus, thereby contributing to disease resistance breeding.

Male sterility is an important trait for breeding and for the seedless fruit production in citrus. We identified one seedling which exhibiting male sterility and seedlessness (named ms1 hereafter), from a cross between two fertile parents, with sour orange (Citrus aurantium) as seed parent and Ponkan mandarin (Citrus reticulata) as pollen parent. Analysis using pollen viability staining, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) revealed that the mature pollen of the ms1 was aborted, displaying collapse and deformity. Further cytological analysis identified the abnormal formation of monad, dyad, and tetrad instead of the normal tetrad formation, leading to meiotic failure in the seedless hybrid. By comparative transcript profiling of meiotic anther of fertile and sterile hybrids, we observed significant downregulation of CYCA1;2 (TAM) and OSD1 genes in the hybrid, which known to control the transition from meiosis I to meiosis II in plants. These results indicated abnormal meiosis led to the male sterility of the seedless hybrid and that the decreased activities of kinases and cyclins may associated with the failure of the transition of meiosis I to meiosis II during anthers development.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01521-5.

The Dasypyrum genus species are found predominantly in the Mediterranean region. They possess an array of agronomically essential traits, such as resistance to biotic and abiotic stresses, high protein content, and better grain quality, and are thus a valuable genetic resources for wheat improvement. In recent decades, there has been significant progress in the development of wheat-Dasypyrum genetic stocks, leading to the successful transfer of beneficial genes from Dasypyrum into cultivated wheat. Notably, the chromosome-scale genome assembly of Dasypyrum villosum was preliminarily completed in 2023, laying the groundwork for functional genomics research and wheat-Dasypyrum introgression breeding. This article aims to provide a concise overview of the relationships between different species belonging to the Dasypyrum genus, the development of wheat-Dasypyrum genetic stocks, the desirable genes derived from Dasypyrum, and the molecular and cytogenetic markers that could be used to identify Dasypyrum chromatins. These insights can assist wheat breeders in utilizing the Dasypyrum genus in future wheat breeding endeavors.

Leaves play a critical role in plant growth and development, directly influencing crop yield through their essential functions in photosynthesis and respiration. This study employed inheritance analysis and gene mapping of an F₂ population derived from a cross between a spontaneous yellow-green leaf tomato mutant and a wild-type tomato line. The findings conclusively demonstrated that the yellow-green leaf trait is controlled by a single recessive gene. Subsequent fine-mapping localized this gene to a 270-kb region on chromosome 12 of the reference Heinz 1706 genome. Annotation and functional characterization of genes within this region indicated Solyc12g009470 (yg-2) as the primary candidate gene influencing the yellow-green phenotype trait. Sequencing analysis revealed a 49-bp deletion in the first exon of yg-2, resulting in suppressed yg-2 expression. This functional role was further confirmed through Solyc12g009470 gene editing in tomatoes. Moreover, comparative analyses of photosynthetic pigments and chloroplast ultrastructure revealed notable differences between the mutant and the wild-type lines. Furthermore, the mutant exhibited reduced photosynthetic rate and yield-related agronomic traits. These findings provide valuable insights into the molecular mechanisms underlying yellow-green leaf formation in tomatoes.

This study delves into the genetic mechanisms underlying seed coat color variation in cowpeas (Vigna unguiculata [L.] Walp.), a trait with significant implications for nutritional value, consumer preference, and adaptation to environmental stresses. Through a genome-wide association study (GWAS) involving cowpea accessions exhibiting red, green, and blue seed coats, we identified 16 significant single nucleotide polymorphisms (SNPs) distributed across chromosomes 3, 4, 5, 9, 10, and 11. Our analysis highlighted the polygenic nature of seed coat color, emphasizing the shared SNP loci across different colors, suggesting integrated genetic influence or linked inheritance patterns, especially on chromosomes 9 and 10. We highlighted candidate genes, including Pentatricopeptide repeat family (PPR), Lupus La-related protein/La-related protein 1, and Udp-glycosyltransferase 71b2-related genes on chromosome 9, and MYB-like DNA-binding (MYB) genes on chromosome 10, all of which are implicated in pigment biosynthesis and regulatory pathways crucial to seed coat coloration and plant physiological processes. Our results corroborate previous findings linking seed coat color to the anthocyanin biosynthesis pathway and reveal the complex genetic architecture and phenotypic plasticity inherent in cowpeas. The overlap in quantitative trait loci (QTL) regions across different seed coat colors points to a shared genetic basis, potentially enabling the manipulation of seed coat color to enhance the nutritional profile and marketability of cowpeas.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01516-2.

Plant height is one of the most critical factors influencing wheat plant architecture, and the application of Green Revolution genes has led to a reduction in plant height and an increase in yield. Discovering new dwarfing genes and alleles can contribute to enhance the genetic diversity of wheat. Here we obtained an EMS induced dwarf wheat mutant je0166 with increased grain weight, which exhibited a reduction in plant height ranging from 46.47% to 49.40%, and its cell length was shorter. The mutant je0166 was sensitive to exogenous gibberellin, but its sensitivity was lower than that of its wild type. Genetic analysis on plant height and gene mapping located the target region to a 4.07 cM interval on chr. 4AL. Within this interval, we identified a co-segregated mutation in Rht-A1h, which is a novel allele of the Green Revolution gene Rht-A1. We also found large fragment inversions in the genetic map of the mutant. The novel allele diversifies natural allelic variations and could be utilized in future wheat improvement. Furthermore, we demonstrated that chemical mutagen treatment led to large fragment inversion.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01515-3.

Coleoptile length, in wheat, is a significant agronomic trait impacting yield by facilitating the successful establishment of seedlings. In arid regions, varieties possessing longer coleoptile can evade harsh conditions by deep sowing, paving the way for improved yield. However, the study of genes involved in coleoptile development is insufficient. In this study, a high-density 660 K SNP array was used for genome-wide association study (GWAS) on coleoptile length in 150 wheat varieties. The findings revealed the detection of 353 significantly associated SNPs across all environments. The integration of linkage disequilibrium analysis and haplotype analysis mined 23 core QTLs capable responsible for the stable regulating coleoptile length in wheat. In wheat varieties characterized by extended coleoptile length, 6,600, 11,524, and 6,059 genes were found to be differentially expressed at three distinct developmental stages within the coleoptile, respectively. Through GWAS, gene expression levels, and functional annotation, we concluded the identification of two candidate genes (TraesCS2B02G423500, TraesCS2B02G449200) regulating wheat coleoptile length. By employing WGCNA and protein interactions prediction, discovered that the 19 genes were found to interact with candidate genes and participate in plant hormone metabolism and signaling, cell elongation or proliferation, which collectively contributing to coleoptile elongation. Additionally, two KASP markers were developed which can be used in breeding. These results offer a basis for understanding the genetic regulatory network responsible for wheat coleoptile length formation. The QTLs and candidate genes identified in this study can be further utilized for genetic improvement of wheat coleoptile length.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01520-6.

Citrus Huanglongbing (HLB) is a devastating disease spread by citrus psyllid, causing severe losses to the global citrus industry. The transmission of HLB is mainly influenced by both the pathogen and the citrus psyllid. The unculturable nature of the HLB bacteria (Candidatus Liberibacter asiaticus, CLas) and the susceptibility of all commercial citrus varieties made it extremely difficult to study the mechanisms of resistance and susceptibility. In recent years, new progress has been made in understanding the virulence factors of CLas as well as the defense strategies of citrus host against the attack of CLas. This paper reviews the recent advances in the pathogenic mechanisms of CLas, the screening of agents targeting the CLas, including antimicrobial peptides, metabolites and chemicals, the citrus host defense response to CLas, and strategies to enhance citrus defense. Future challenges that need to be addressed are also discussed.

Cabbage is a widely cultivated leafy vegetable, but head rot disease caused by the fungus Sclerotina sclerotiorum can seriously reduce its yield and quality. There are currently not any cabbage varieties that are completely immune to the disease, but its wild relative Brassica incana is very resistant. In this study, cabbage resistance was improved by backcrossing a highly resistant B. incana accession (C01) with a susceptible cabbage cultivar (F416). Although C01 lacks a leafy head formation, highly resistant plants appeared in the fourth backcrossing generation (BC₄F₁) that had a similar leafy head to F416. The individuals with strong resistance were purified by self-pollination. Inbred lines that maintained a relatively stable resistance at BC₄F₃ were developed and had significantly higher resistance to S. sclerotiorum than F416. In addition, hybrids created from a cross between of BC₄F₃ and E2 had higher resistances to S. sclerotiorum and similar agronomic characteristics to Xiyuan 4. The results demonstrated that new F416 lines that are resistant to S. sclerotiorum can be developed, and that these lines could be used to create new cabbage varieties with superior head rot resistance.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01513-5.