Theoretical and Applied Genetics最新文献

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.

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.