Theoretical and Applied Genetics最新文献

Key message: We analysed the chromosomal structures of two wheat-Thinopyrum intermedium addition lines Z4 and Z5 and resolved the linkage relationship between the leaf rust and stripe rust resistance genes in Z4. Wheat addition lines Z4 and Z5 carrying rust resistance genes from Thinopyrum intermedium (JJJ^sJ^sStSt, 2n = 6x = 42) together with three wheat lines involved in the production of these addition lines were analysed by rust response, 90K SNP genotyping, and molecular cytogenetic analysis. Seedling leaf rust (LR) responses to five diverse pathotypes indicated that the LR resistance gene(s) was located in translocation chromosome T3DS-3AS.3AL-7StS common to Z4 and Z5. The stripe rust (YR) resistance gene(s) was located in translocation chromosome T3AL-7StS.7StL, which is unique to Z4, based on the seedling YR responses to four diverse pathotypes. Backcross and selfed populations involving the addition lines and various wheat cultivars were studied to understand the inheritance of the alien resistance genes. Although inheritance studies indicated genetic linkage, the alien genes for resistance to leaf rust (LR) and stripe rust (YR) in Z4 were present in different wheat-Th. intermedium translocation chromosomes. We found that LR and YR were in pseudo-linkage, rather than true linkage.

Keymessage: GBS read coverage analysis identified a Robertsonian chromosome from two Thinopyrum subgenomes in wheat, conferring leaf and stripe rust resistance, drought tolerance, and maintaining yield stability. Agropyron glael (GLAEL), a Thinopyrum intermedium × Th. ponticum hybrid, serves as a valuable genetic resource for wheat improvement. Despite its potential, limited knowledge of its chromosome structure and homoeologous relationships with hexaploid wheat (Triticum aestivum) has restricted the full exploitation of GLAEL's genetic diversity in breeding programs. Here, we present the development of a 44-chromosome wheat/GLAEL addition line (GLA7). Multicolor genomic in situ hybridization identified one chromosome arm from the St subgenome of Th. intermedium, while the other arm remained unclassified. Genotyping-by-sequencing (GBS) read coverage analysis revealed a unique Robertsonian translocation between two distinct Thinopyrum subgenomes, identified as 4StS·1J^vsS. The GLA7 line demonstrated strong adult plant resistance to both leaf rust and stripe rust under natural and artificial infection conditions. Automated phenotyping of shoot morphological parameters together with leaf relative water content and yield components showed that the GLA7 line exhibited elevated drought tolerance compared to parental wheat genotypes. Three years of field trials showed that GLA7 exhibits similar agronomic performance and yield components to the wheat parents. This unique addition line holds promise for enhancing wheat's tolerance to multiple stresses through the introduction of new resistance genes, as well as its ability to mitigate the effects of temporary water limitation during flowering, all without negatively impacting wheat performance.

Key message: A dwarf mutant with short branches (csdf) was identified from EMS-induced mutagenesis. Bulked segregant analysis sequencing and map-based cloning revealed CsKAO encoding ent-kaurenoic acid oxidase as the causal gene. Plant architecture is the primary target of artificial selection during domestication and improvement based on the determinate function for fruit yield. Plant architecture is regulated by complicated genetic networks, more underlying mechanism remains to be elucidated. Here, we identified a dwarf mutant (csdf) in an EMS-induced cucumber population, and genetic analysis revealed the mutated phenotype is controlled by a single recessive gene. Optical microanalysis showed the decrease in cell length is mainly contribute to the dwarf phenotype. By strategy of BSA-seq combined with map-based cloning, CsaV3_6G006520 (CsKAO) on chromosome 6 was identified as the candidate gene for csdf. Gene cloning and sequence alignment revealed a G to A mutation in the sixth exon, which causes the premature stop codon in CsKAO of csdf. Expression analysis revealed CsKAO was expressed in various tissues with abundant transcripts, and has significant differences between WT and csdf. Gene annotation indicated CsKAO encodes a cytochrome P450 family ent-kaurenoic acid oxidase which functioned in GA biosynthesis. GA-relevant analysis showed that endogenous GA contents were significantly decreased and the dwarfism phenotype could be restored by exogenous GA₃ treatment; while, some of the representative enzyme genes involved in the GA pathway were up-regulated in csdf. Besides, IAA content is decreased in the terminal bud and increased in the lateral bud in csdf as well as several IAA-related genes are differentially expressed. Overall, those findings suggest that CsKAO regulated plant height via the influence on GAs pathways, and IAA might interact with GAs on plant architecture morphogenesis in cucumber.

Key message: We have identified a unique genetic locus for seed shattering in Italian ryegrass that has an exceedingly large effect and shows partial dominance for reduced seed shattering. Genetic improvement of seed retention in forage grasses can contribute to improving their commercial seed production. The objective of this study was to identify the genetic loci responsible for seed shattering in Italian ryegrass (Lolium multiflorum Lam.) using F₂ and F₃ progeny from a cross between a reduced shattering genotype and a self-fertile shattering genotype. High negative correlations (- 0.622 in F₂ and - 0.737 in F₃) were found between two methods of measuring shattering: (1) the percentage of seed shattering obtained by manually stripping the spike and (2) the non-basal floret breaking tensile strength (BTS). On the other hand, basal floret BTS showed a non-significant (F₂) or low (- 0.226 in F₃) correlation with the percentage of seed shattering by stripping. We identified a quantitative trait locus (QTL) near the start of linkage group 2, designated as qSH2.1, which was associated with both seed shattering measured by stripping and non-basal floret BTS with exceptionally high LOD values (11.0-34.0); in addition, we detected five minor QTLs. qSH2.1 explained about 2/3 of the total variation in the percentage of seed shattering by stripping at the late dough stage in the F₂ population. The reduced shattering trait was partially dominant, in contrast to the genetic mode in many previous reports on other crops. Candidate orthologs for the previously reported seed shattering genes were not found near the qSH2.1 locus in the ryegrass genome, suggesting that this QTL may be due to a yet-undiscovered gene.

Key message: GWAS of a new MAGIC population containing alleles from five tetraploid Gossypium species identified novel fiber QTL and confirmed previously identified stable QTL. Identification of loci and underlying genes for fiber quality traits will facilitate genetic improvement in cotton fiber quality. In this research, a genome-wide association study (GWAS) was carried out for fiber quality attributes using a new multi-parent advanced generation inter-cross (MAGIC) population consisting of 372 recombinant inbred lines (RILs). Sixteen parents including 12 exotic germplasm lines derived from five tetraploid Gossypium species and 4 Upland cotton varieties were intercrossed to develop the population. Both RILs and parental lines were evaluated at three locations, College Station, Texas; Las Cruses, New Mexico; and Stoneville, Mississippi, from 2016 through 2023. Fiber length (UHM) had positive correlation with strength (STR) and length uniformity (UNI) and a negative correlation with micronaire (MIC) and elongation (ELO). By combining all the data from all locations, we identified significant SNPs for ELO, UHM, and UNI while STR and MIC were location dependent. These results suggest an important role of genotype by environment interaction in a GWAS of fiber traits. Twenty possible novel fiber QTL were identified: 10 for STR, three for UNI, and seven for MIC. The QTL for ELO (Chr.D04: 53-Mb), UHM (Chr.D11: 24-Mb), and UNI (Chr.D04: 34-Mb) were stable across multiple environments and may be useful for marker-assisted selection to improve fiber quality. For STR, we found candidate genes Gh_A07G1574 and Gh_A07G1581 to be present in the previously identified QTL region (Chr.A07: 77-Mb) on chromosome A07. Identified loci and their corresponding candidate genes will be useful to improve fiber quality via marker-assisted selection in a cotton breeding.

Key message: The dQTG.seq model was utilized to investigate the genetic underpinnings of phenotypic plasticity in soybean isoflavone content, leading to the identification of 100 marker sites associated with phenotypic plasticity, including 27 transcription factors. Overexpression of Glyma.18G091600 (GmERF7) hairy roots under low temperature, salt, and drought stress confirmed the regulatory role of GmERF7 in the phenotypic plasticity of soybean isoflavone content. Phenotypic plasticity is characteristic of organisms that undergo phenotypic changes in response to environmental fluctuations. This phenomenon is pivotal in evolutionary processes and the emergence of new traits. Isoflavones, significant secondary metabolites found in soybeans, have garnered considerable attention owing to their beneficial physiological effects on human health. The variation in isoflavone content among different soybean varieties is influenced by diverse environmental factors, thereby influencing the evaluation of high and low isoflavone varieties. In this study, we measured the phenotypic plasticity of isoflavone content in recombinant inbred lines Hefeng 25 and L-28 in three different environments over two years. Utilizing the dQTG.seq model, 100 statistically significant markers were identified, and 101 potential genes, including 27 transcription factors, were screened. Through qRT-PCR analysis, elevated expression levels of Glyma.18G091600, Glyma.09G196200, and Glyma.05G229500 were observed in various parts of soybean plants. Under low temperature, drought or salt stress conditions, the related enzymes involved in the isoflavone synthesis pathway were notably upregulated in Glyma.18G091600 (GmERF7) overexpressed hairy roots compared to wild-type controls, resulting to higher phenotypic plasticity values for DZ, GC, GT, and TI. These results suggest that GmERF7 influences the phenotypic plasticity of soybean isoflavone content, enhancing adaptation to adverse environments, while also promoting the synthesis and accumulation of soybean isoflavones.

Key message: Three computationally efficient algorithms of GP including RHBK, RHDK, and RHPK were developed in approximate genome-based kernel model. The drastically growing amount of genomic information contributes to increasing computational burden of genomic prediction (GP). In this study, we developed three computationally efficient algorithms of GP including RHBK, RHDK, and RHPK in approximate genome-based kernel model, which reduces dimension of genomic data via Nyström approximation and decreases the computational cost significantly thereby. According to the simulation study and real datasets, our three methods demonstrated predictive accuracy similar to or better than RHAPY, GBLUP, and rrBLUP in most cases. They also demonstrated a substantial reduction in computational time compared to GBLUP and rrBLUP in simulation. Due to their advanced computing efficiency, our three methods can be used in a wide range of application scenarios in the future.

Key message: Mutations in the CsEMS1 gene result in male sterility and reduced wart number and density. Male sterility and fruit wart formation are two significant agronomic characteristics in cucumber (Cucumis sativus), yet knowledge of our underlying genetics is limited. In this study, we identified an EMS-induced male sterility and few small warts mutant (msfsw). Histological observations revealed defects the absence of tapetum, meiotic aberration and impaired microspore formation in the anthers of the mutant. The mutant also exhibits a reduction in both the size and number of fruit spines and fruit tubercules. Genetic analysis revealed that a single recessive gene is responsible for the mutant phenotypes. BSA-Seq and fine genetic mapping mapped the msfsw locus to a 63.7 kb region with four predicted genes. Multiple lines of evidence support CsEMS1(CsaV3_3G016940) as the candidate for the mutant allele which encodes an LRR receptor-like kinase, and a non-synonymous SNP inside the exon of CsEMS1 is the causal polymorphisms for the mutant phenotypes. This function of CsEMS1 in determination of pollen fertility was confirmed with generation and characterization of multiple knockout mutations with CRISPR/Cas9 based gene editing. In the wild-type (WT) plants, CsEMS1 was highly expressed in male flowers. In the mutant, the expression level of CsEMS1, several tapetum identity-related genes, and trichome-related genes were all significantly reduced as compared with the wild-type. Protein-protein interaction assays revealed physical interactions between CsEMS1 and CsTPD1. Quantitation of endogenous phytohormones revealed a reduction in the ethylene precursor ACC in CsEMS1 knockout lines. This work identified an important role of CsEMS1 in anther and pollen development as well as fruit spine/wart development in cucumber.

Key message: Restoration of haploid female and haploid male fertility without colchicine is feasible. Three SNPs and eight gene models for HFF, and one SNP and a gene model for HMF were identified. Doubled haploid (DH) breeding accelerates the development of elite inbred lines and facilitates the incorporation of exotic germplasm, offering a powerful tool for maize improvement. Traditional DH breeding relies on colchicine to induce haploid genome doubling. Colchicine is toxic, and its application is labor-intensive, with most genotypes recording low genome doubling rates (10-30%). This study investigates spontaneous haploid genome doubling (SHGD) as a safer and more efficient alternative to colchicine. We evaluated the effectiveness of SHGD in restoring haploid female fertility (HFF) and haploid male fertility (HMF) without colchicine. Using genome-wide association studies (GWAS), we identified genomic regions influencing HFF and HMF. The plant materials included the BS39-haploid isogenic lines (HILs) and BS39-SHGD-haploid isogenic lines (HILs). Our results revealed significant SNP associations for both traits, with candidate genes involved in cell cycle regulation, cytoskeletal organization, and hormonal signaling. Analysis of variance (ANOVA) revealed significant variation in HFF across haploids and two environments. Similarly, HMF showed substantial differences across haploids and between the two environments. Spearman correlation between HFF and HMF showed no correlation (r = -0.03) between the two traits. HFF showed high heritability (0.8), indicating strong genetic control, whereas HMF displayed moderate heritability (0.5), suggesting additional environmental influences. The findings underscore the potential of SHGD to enhance DH breeding efficiency and support the development of new maize varieties tailored to diverse agricultural needs.