Theoretical and Applied Genetics最新文献

Key message: This study identified efficient marker combinations consisting of two significant SNPs associated with salt tolerance in cowpea, providing genomic insights and candidate frameworks for future validation and breeding applications. Salt stress is a major abiotic factor that severely reduces crop productivity, particularly in arid and semi-arid regions. Its effects are further exacerbated by climate change and the continuous buildup of salts in the soil. Although cowpea (Vigna unguiculata L.) is regarded as a promising crop in drought- and heat-prone areas, it remains especially susceptible to salt stress during its early developmental stages. To investigate the genetic foundation of salt tolerance, a genome-wide association study (GWAS) was carried out using 401 genetically diverse cowpea germplasms. This analysis integrated phenotypic assessments under 200 mM NaCl treatment at the early vegetative stage with 34,704 high-quality single-nucleotide polymorphisms (SNPs). Four morpho-physiological traits were chosen to assess responses to salt stress, including leaf scorch score (LSS), leaf chlorophyll content (LCC), and the contents of leaf sodium ions (LSI) and leaf chloride ions (LCI). GWAS identified several significant marker-trait associations, among which six SNPs with the highest statistical significance across the four traits were selected. Candidate genes associated with these SNPs were involved in ion transport, regulation of reactive oxygen species (ROS), and secondary metabolite biosynthesis, which are fundamental mechanisms in salt tolerance. Moreover, the combination of two SNPs, 2_52855 and 2_38343, proved to be the most effective marker for distinguishing salt-tolerant germplasms. Germplasms containing the GC genotype at this combination, meaning the G allele at the SNP 2_52855 and the C allele at the SNP 2_38343, consistently demonstrated enhanced salt tolerance. These findings enhance our understanding of the genetic architecture of salt stress response in cowpea and provide a foundation for identifying molecular markers that can be validated and applied in future breeding efforts.

Key message: Through the integration of GWAS and RNA-seq analysis, three candidate genes associated with unsaturated fatty acids were identified in soybean. Heterologous overexpression of these genes in Arabidopsis confirmed their functions in altering seed fatty acid profiles. As a major source of the world's vegetable oil, the nutritional value and storage stability of soybean oil are largely determined by the relative contents of unsaturated fatty acids (UFAs). However, the genetic regulations of UFAs in soybean remains incompletely understood. To elucidate the regulatory mechanisms governing UFAs in soybean seed, a panel of 312 soybean accessions was evaluated across five environments, and a genome-wide association study (GWAS) was performed to identify quantitative trait loci (QTLs) for UFA traits. A total of 52 stable QTLs were detected in at least two environments, including 20, 16 and 16 QTLs associated with oleic acid (OA), linoleic acid (LA) and linolenic acid (LNA), respectively. Of them, qOA10-4 and qLNA13-2 were consistently detected across four environments, while qOA13-2/qLA13-1 and qLA15-1/qLNA15-1 exhibited pleiotropic effects. Candidate gene analysis within 50 kb flanking regions of lead SNPs identified 189 genes, including 61, 56 and 93 genes for OA, LA and LNA, respectively. Integrated analysis of GWAS and transcriptome data revealed 41 candidate genes showing significant differential expression between the lines with divergent UFA profiles. Sequence comparison of three prioritized candidates, GmABH, GmCFE, and GmPI-PLC, identified a key non-synonymous SNP in the GmABH coding region and promoter variations in all three candidates. Heterologous overexpression in Arabidopsis confirmed that all three candidate genes significantly altered the UFA profiles of the Arabidopsis seeds. The QTLs and candidate genes identified in this study might be useful for the improvement of UFAs in soybean.

Seed oil content (SOC) of oilseed rape (Brassica napus L.) is an important agricultural trait that is controlled by a complex regulatory mechanism. In this study, we performed integrated analyses of Genome-Wide Association Studies (GWAS) and Target Induced Local Lesions in Genomes (TILLING) to explore genetic loci/mutant alleles associated with SOC in rapeseed. GWAS analysis of a diverse panel of 324 accessions identified 142 SOC-associated quantitative trait loci (QTLs). Of them, qSOC.C06.4 encompassed the HD-ZIP transcription factor BnaC.GL2.b, which may regulate oil accumulation predicted by haplotypes analysis. An EMS (ethylmethanesulfonate)-TILLING platform that consists of 4,734 M₂ plants was constructed to identify the mutants of BnaC.GL2.b in rapeseed. Five mutant alleles of BnaC.GL2.b were identified using TILLING, of which three missense mutants exhibited higher SOC than the controls (two nonsense mutants). In addition, we measured SOC of 9332 M₂ plants ranging from 22.06% to 51.00%, with the average of 38.19%. Together, we propose to use GWAS combined with TILLING to identify causal genes and mutant alleles for a quantitative trait in the polyploid rapeseed. Furthermore, our new rapeseed germplasm resources may be useful for mutation breeding.

Key message: Identified and validated stable QTL for spike traits across 15 environments, promising candidate genes for thermotolerance and spike traits, novel KASP and gene-based markers, providing genomic resources for breeding high-yielding, heat-tolerant wheat. To unravel the genetic architecture of six spike traits under heat stress, we used a doubled haploid (DH) mapping population (177 lines), developed from a cross between a heat-sensitive cultivar (PBW343) and a heat-tolerant genotype (KSG1203). This DH population and the two parents were phenotyped for six spike traits under timely, late, and very late sown conditions, over three years and two locations (total 15 environments). Best linear unbiased estimates for each trait and a genetic map (5,710 SNP markers) were used for QTL mapping. A total of 51 QTL were detected under timely (17), late (10), and very late (18) sown conditions, with six QTL common across fifteen environments. These QTL explained phenotypic variation ranging from 7.1% (QFf.ccsu-7B) to 23.6% (QSl.ccsu-6A). All identified QTL were successfully integrated into the wheat physical map. A set of 14 stable, major QTL was validated in high-yielding DH lines and recommended for marker-assisted recurrent selection for wheat improvement in optimal/heat stress conditions. Several QTL co-localized with known genes responsible for important traits including grain yield (TaGW2-B1, PI1-1B/WPI-1-1B). Seventy heat-responsive candidate genes associated with 38 QTL were identified, which encode 33 distinct proteins. A KASP marker was developed for the floret fertility QTL (QFf.ccsu-3A), and gene-based functional SSR markers were developed for the five important candidate genes alongside the discovery of Indels and SNPs in seven candidate genes having a role in heat tolerance. The generated genomic resources could be used in future studies and to breed heat-tolerant, high-yielding wheat varieties and germplasm.

Key message: Field-based phenotyping of root system architectural (RSA) traits in a diversity panel (PI-GAP) of pigeonpea was conducted across three diverse pigeonpea growing environments along with identification of genomic regions associated with these traits through GWAS analysis. Root system architecture (RSA) plays a crucial role in plant stress tolerance mechanisms serving as the main route for water and nutrient acquisition, while also mediating plant-rhizosphere signalling. In the current study, an attempt was made to understand the genetic variability and genomic regions associated with RSA traits, as a relatively unexplored area of research in pigeonpea. The field-based "Shovelomics" approach was utilized to phenotype eight RSA traits: tap root length (TRL), lateral root length (LRL), number of lateral roots (NRL), stem diameter (SD), root diameter (RD), root angle from first and second lateral roots (RA1 and RA2) and root fresh weight (RFW) at physiological maturity. The pigeonpea international genome-wide association panel (PI-GAP) comprising of 185 genotypes from the reference set and 15 elite genotypes were used in the study. The combined ANOVA revealed significant genetic variance for all RSA traits except for RA2. Genome-wide association study was conducted using the Axiom Cajanus 56 K SNP array, leading to identification of 45 marker trait associations (MTAs) associated with RSA traits in pigeonpea. Multi-locus GWAS models detected six MTAs accounting for 4.84% to 18.73% of the phenotypic variation estimated (PVE) for TRL, 12 MTAs for LRL (4.73-13.92% PVE) and 11 MTAs for NLR (3.03-14.03% PVE value), respectively. Candidate gene analysis revealed genes associated with these traits, including BAG (Bcl-2-Associated athanogene) family molecular chaperone regulator 6 (CcLG01_17476096 and CcLG01_17476721), root cap (CcLG04_5972718) and Protein MAINTENANCE OF MERISTEMS (MAIN) (CcLG06_8242342). These genes were found to have key roles in growth and establishment of roots under stress-related conditions in model crops. Further validation of identified MTAs would provide an opportunity to develop trait-specific markers paving the way for marker-assisted breeding in pigeonpea. Based on RSA traits, pigeonpea genotypes were categorized into deep, spreading and dimorphic root system. These classifications facilitate the phenotypic selection of genotypes for breeding against drought, heat, waterlogging and salinity adaptation. Improved cultivars with an ideal root architecture designed for efficient resource uptake and high yield under diverse environments could help address food security challenges in semi-arid tropics.

Key message: We identified GhTPS11 as a positive regulator of flowering in cotton through integrating QTL mapping, transcriptomic analysis and functional assays. Early maturity is one of the most essential targets in cotton breeding improvement. Enhancing early maturity can facilitate cotton rotation, thereby increasing the multiple cropping index and land use efficiency. The early-maturity trait is closely associated with key agronomic characteristics such as flowering time (FT) and plant height (PH). In this study, we identified 11 QTLs for FT and PH, including a QTL cluster on chromosome D08 (Chr. D08), using a recombinant inbred line (RIL) population derived from a cross between the early-maturing cultivar LMY19 and the late-maturing cultivar LMY37. Through integrated analysis of transcriptome data and DNA sequence variation, GhTPS11 (trehalose-6-phosphate synthase 11) was identified as a key candidate gene. Heterologous expression of GhTPS11 in Arabidopsis resulted in significantly earlier bolting in transgenic lines compared to the wild type (WT). Conversely, silencing GhTPS11 in cotton via virus-induced gene silencing (VIGS) delayed both squaring and flowering, indicating that GhTPS11 acts as a positive regulator of flowering in cotton. RNA-seq analysis suggested that GhTPS11 integrates carbon metabolism with the age pathway via trehalose-6-phosphate (Tre6P) signaling to control flowering. In summary, this study identifies a causal gene underlying an early-maturity QTL cluster, elucidates its function, and provides a valuable genetic resource and theoretical foundation for molecular breeding in cotton.

Capsule shattering in sesame is a major agronomic constraint that reduces yield stability and limits mechanized harvesting efficiency. To address this challenge, 200 genetically diverse sesame genotypes from Sudan were genotyped using genotyping-by-sequencing (GBS) and evaluated for three consecutive seasons under field conditions for shattering type (ST), type of capsule beak (TCB), and bicarpellate capsule shape (BS). The resulting phenotypic and genotypic data were integrated into a multi-model genome-wide association study (GWAS) framework (BLINK, FarmCPU, and MLMM) to elucidate the genetic architecture of capsule-shattering traits. Two marker-trait associations (MTAs) were consistently identified across the GWAS models, comprising Chr1_19419575 associated with the TCB and Chr2_15649330 linked to ST. Additional MTAs, including Chr8_31466064 for ST and Chr8_19392181 and Chr8_30292484 for TCB, were also detected in this study, further highlighting the complex genetic regulation of capsule traits. Allelic effect analysis further validated the functional role of key allelic variants at Chr2_15649330 and Chr8_31466064, demonstrating significant differences in shattering responses among genotypic subgroups. In silico functional enrichment analysis using a candidate gene approach identified 68 homologous genes associated with pod shattering in Brassica napus, of which FLZ3, RZF1, MKK5, and COR27 showed distinct expression patterns that correlated with shattering susceptibility during pod development. These results provide new insights into the genetic regulation of capsule shattering, providing valuable targets for marker-assisted selection and development of sesame cultivars with enhanced resistance to shattering.

Key message: Anthocyanin deficiency in eggplant peel results from natural variation at the SmFAP1 locus, involving a 6-bp deletion that disrupts DNA binding and a second loss-of-function allele, which enables marker-assisted selection. Anthocyanins, the pigments responsible for purple coloration in eggplant peels, significantly influence consumer preference and market value. However, the genetic basis of natural variation in this trait, particularly the functional impact of allelic mutations, remained poorly characterized. In this study, we found that anthocyanin presence is controlled by a single dominant gene, which co-localized with a known QTL FAP10.1. Using BSR-seq and linkage mapping, we identified SmFAP1, encoding an R2R3-MYB transcription factor, as the causal gene in this locus. Sequence analysis of the non-functional allele, Smfap1-1, from a green-peel parent revealed a 6-bp in-frame deletion that removes two amino acids (R44 and A45) from the R2R3-MYB domain. Functional validation through transient expression in Nicotiana benthamiana and stable transformation in tomato showed that SmFAP1 activates anthocyanin biosynthesis genes and promotes anthocyanin accumulation, while Smfap1-1 fails to do so. Further molecular assays confirmed that this loss-of-function is caused by the disruption of the protein's capacity to bind the promoters of key anthocyanin structural genes. A co-dominant CAPS marker targeting this 6-bp InDel shows a significant association with peel color variation across 238 eggplant germplasms, confirming its contribution to natural variation. Furthermore, an additional loss-of-function allele, Smfap1-2, was identified in other non-purple accessions lacking this deletion, carrying both a 26-bp deletion that disrupts splicing and a frameshift insertion leading to a premature stop codon. Our findings offer valuable insights into the genetic basis of peel color variation and provide a practical tool for marker-assisted breeding to enhance fruit quality and nutritional traits.

The development of oat cultivars with resistance to crown rust caused by Puccinia coronata f. sp. Avenae (Pca) is key for sustainable disease control. This study examined two recombinant inbred line populations, Provena x GS7 and Boyer x GS7, to identify adult plant resistance QTL in Australian fields. Seven distinct QTL associated with rust resistance were identified. KASP markers were developed for single nucleotide polymorphisms (SNPs) tightly linked to the four most significant QTL on chromosomes 4A and 7A. A major QTL named QPc_GS7_4A.2 with a resistance allele derived from line GS7 was mapped to chromosome 4A, overlapping with genomic regions previously associated with both resistance gene Pc61 and adult plant resistance. Genetic mapping for rust resistance at the seedling stage using a subset of Provena x GS7 lines with contrasting alleles at QPc_GS7_4A.2 suggests a role of this locus in seedling resistance, which may be explained by the presence of Pc61. Seedling resistance profiles between GS7 and the Pc61 differential line against 20 Pca isolates, a haplotype analysis of QPc_GS7_4A.2 in the oat crown rust differential set, and a collection of 182 oat lines support this hypothesis, although confirmation needs future research. The KASP markers developed in this study will assist breeders in efficiently integrating the resistance allele for gene combinations in new cultivars.

In sweetpotato, the quantitative variation of anthocyanin accumulation produces a continuous color spectrum that underpins both ornamental appeal and nutritional quality across cultivar species. Although previous studies have established that the expression of IbMYB1 is essential for purple pigmentation in germplasm, this gene exists in multiple copies within the polyploid genome, rendering the resulting genetic complexity incompletely understood to date. Here, we found that hexaploid genome of sweetpotato contains at least five IbMYB1 copies, designated IbMYB1-1, IbMYB1-2a/b, IbMYB1-3 and IbMYB1-4. Gene sequence cloning, transgenic complementation and high-resolution spatial expression analyses revealed that the previously uncharacterized IbMYB1-4 is specifically expressed in the stem cortex and leaf epidermis, where it orchestrates the differential accumulation of distinct anthocyanin monomers, resulting in vines that range from purple to near-black. Yeast one-hybrid screening and dual-luciferase reporter assays confirmed that the bHLH transcription factor IbbHLH2 binds to a canonical G-box motif within the IbMYB1-4 promoter, thereby reinforcing IbMYB1-4 expression. Reciprocal F₁ populations derived from the interspecific hybridizations of 'Purple_X20' × 'X99' and 'Black_leaf' × 'X99' exhibited strict co-segregation between IbMYB1-4 and the single dominant Purple (P) locus which is linked to the purple color of stem. Moreover, the purple-black foliage traits may have been regulated by a dosage-dependent interaction between P locus and a putative R locus, likely attributable to the differential expression of IbMYB1-4. Collectively, these findings provide a novel genetic resource for sweetpotato breeding programs and expand the theoretical framework for the targeted improvement of pigmented germplasm.