Theoretical and Applied Genetics最新文献

Key message: Two novel quantitative trait loci associated with soybean protein content stability were identified on chromosomes 10 and 18. Haplotype analysis showed these to significantly improve stability without protein content penalty. Soybean seed protein content is a complex physiological trait under polygenic control and significant genotype by environment interaction. Protein content is largely influenced by ambient atmospheric temperature at pod-filling, with increased temperatures enhancing seed protein accumulation. The identification of genomic regions associated with protein content stability will facilitate an increased understanding of seed development physiology and assist in the development of more broadly adapted food-grade soybean cultivars. In this work, 210 recombinant inbred lines were derived from the intraspecific cross of the high protein accession BARC_-6 (PI 555396), and the low protein MSU breeding accession E14077 for the investigation of quantitative trait loci associated with protein content and protein content stability across multiple years and test locations. Indices for static protein content stability were used to estimate genome by environment interactions across Northern and Southern soybean production regions. Composite interval mapping returned one stable major effect QTL associated with protein content on chromosome 20 explaining approximately 20.7% of phenotypic variation. Two novel QTLs associated with absolute protein stability were detected on chromosomes 10 and 18, explaining approximately 8.6% and 7.6% of phenotypic variation, respectively. SNP-based haplotype analysis showed simultaneous favorable effects on protein content and stability when desirable alleles for these QTL were pyramided. These results will serve as a valuable tool for the molecular breeding of food-grade soybean cultivars harboring elevated protein content coupled with improved stability across varied environments, thus addressing a key challenge in meeting the global rise in soybean protein demand for both livestock feed and human consumption.

Key message: Yield gaps between variety trials and on-farm yields show diverging trends for grain versus forage maize in Germany in 1987-2023. The yield gap between variety trials and on-farm reduced for grain yield from 30% (1987) to 23% (2023), while for forage maize dry matter yield increased from 15% (1987) to 32% (2023). In variety trials during the same period starch yield in forage maize showed a moderate increase of 14%, while digestibility and starch content did not change over time. N use efficiency in variety trials was improved by 35%, 27% and 18% for grain, dry matter and starch yield, respectively, while N yield in dry matter did not change over time. Maize cultivation increased significantly in Germany over the past 25 years. With a share of over 20% of arable land, maize has become the second most important crop after wheat, primarily due to the growing demand for biogas production. Based on long-term variety trials for grain and forage maize, we quantified breeding progress applying mixed linear models extended by linear and nonlinear regression terms to estimate time trends between 1987 and 2023. Grain yield increased by 33.4 dt ha^-1 (36.3%) and dry matter yield of forage maize by 36.1 dt ha^-1 (19.9%) compared to 1987. Over the last 15 years, there has been a slowdown in upward yield trends. In addition, the NUE of grain and forage maize increased by 35.0% and 27.2%, respectively. From 1987 to 2023, grain yield gaps between variety trials and national on-farm yields reduced from 30.1 to 22.6% while the stagnation of on-farm forage maize yields resulted in an increased yield gap from 15.1 to 32.1%. This diverging trend can be attributed to a complex set of reasons, such as climate change, management practices and economic constraints. Looking at quality traits in the variety trials, starch content and digestibility of forage maize did not change, but starch yield (14.0%) and NUE of starch yield (18.3%) increased, while N yield of forage maize decreased by - 4.7%, though not significant. Our study shows that breeding progress of grain maize was successfully transferred into increasing on-farm yields, while a considerable yield gap remains for forage maize, what calls for additional research.

Key message: The glutathione S-transferase family gene OsGSTT3 in rice regulates seed germination by modulating reactive oxygen species (ROS) homeostasis. The relative expression levels of ROS scavenging-related genes were changed. Seed germination is a complex physiological process regulated by both internal and external factors. Glutathione S-transferases (GSTs), a critical class of antioxidant enzymes, play key roles in plant responses to environmental stress. However, their molecular regulatory mechanisms in rice seed germination remain largely unexplored. In this study, we identified OsGSTT3 as a key regulator of seed germination in rice. Both OsGSTT3 overexpression and knockout lines exhibited delayed germination speeds compared with wild-type (WT) plants. RT-qPCR analysis revealed that OsGSTT3 is highly expressed in seeds and during germination, with its expression modulated by hydrogen peroxide (H₂O₂) and diphenyleneiodonium chloride (DPI). Exogenous H₂O₂ and DPI treatments further confirmed that reactive oxygen species (ROS) levels are critical determinants of germination in OsGSTT3 transgenic lines. Measurements of endogenous H₂O₂ revealed significantly reduced levels in overexpression lines and increased levels in knockout lines relative to WT. Additionally, OsGSTT3 regulates ROS homeostasis during germination by modulating the expression of ROS scavenging-related genes. Collectively, our findings establish OsGSTT3 as a key regulator of seed germination via ROS homeostasis, providing novel insights into the molecular mechanisms of rice germination and offering a potential genetic resource for improving rice germplasm.

Key message: Map-based cloning and gene editing confirmed that ClChlH was the causal gene controlling yellow rind color in watermelon. Fruit rind color is a crucial agronomic trait influencing the commercial quality of watermelon (Citrullus lanatus). Although yellow rind is an important phenotype, its underlying molecular mechanisms remain poorly understood. In this study, genetic analysis using two mapping populations derived from crosses between a yellow rind line (W-21-4-2) and two green rind lines (W-21-301 and W-21-129) indicated that the yellow rind trait is controlled by a single dominant locus, ClYR. By combining BSA and KASP genotyping, we initially mapped ClYR to a 6.5 Mb region on chromosome 4. Subsequent fine mapping with 1345 F_2:3 individuals narrowed the candidate interval to 325.37 Kb, which contains 10 annotated genes. Among these, ClChlH (Cla97C04G068530) emerged as the most promising candidate gene due to multiple insertions/deletions (InDels) in its promoter region that distinguish the yellow and green rind lines. Expression analysis revealed significantly reduced ClChlH transcript levels in the yellow rind line W-21-4-2. Promoter activity assays further demonstrated that these structural variations suppress transcriptional activation of ClChlH. Haplotype analysis confirmed that these promoter InDels were correlated with yellow rind phenotype. Functional validation via CRISPR/Cas9-mediated mutagenesis generated mutants exhibiting yellow-green or sectored (half-green-half-yellow) pigmentation in both rind and leaf tissues. Collectively, our findings elucidate a key genetic regulator of rind coloration and provide valuable molecular resources for future watermelon breeding programs.

Key message: A major QTL conferring powdery mildew resistance was fine mapped to a 54.8 kb region on chromosome 2 using an interspecific RIL population (Citrullus mucosospermus × Citrullus lanatus). Four co-segregating KASP markers were developed and validated across multiple populations, demonstrating their utility for marker-assisted selection. Powdery mildew, caused by Podosphaera xanthii, is a major fungal disease that significantly affects watermelon production worldwide. Developing resistant cultivars through marker-assisted selection (MAS) offers an effective and sustainable strategy for disease management. In this study, a 54,772 bp quantitative trait locus (QTL) associated with powdery mildew resistance was mapped to chromosome 2 (30,111,475-30,166,247 bp) using an F₁₁ recombinant inbred line (RIL) population derived from an interspecific cross between the resistant C. mucosospermus line USVL531-MDR and the susceptible C. lanatus line USVL677-PMS. Genetic analysis revealed that resistance is controlled by a single dominant gene, supported by a 3:1 segregation ratio observed in F₂ populations. The mapped region harbored three lipoxygenase (LOX) genes and one 50S ribosomal protein L27-like gene. Four KASP markers were developed from SNPs located within four putative genes in the QTL region and were validated across multiple segregating populations, including the RIL (USVL531-MDR × USVL677-PMS) and two F₂ populations (USVL531-MDR × 'Sugar Baby' and PI 560003 × USVL677-PMS). These markers accurately differentiated resistant and susceptible individuals (R2 = 0.68-0.82) and exhibited 100% co-segregation with powdery mildew resistance in the RIL and two F₂ populations, demonstrating their utility for MAS. The identified QTL and validated KASP markers will facilitate MAS for powdery mildew resistance breeding and enable future gene cloning work.

Oat crown rust, caused by the fungus Puccinia coronata f. sp. avenae (Pca), is the most destructive foliar pathogen of oat. Almost 100 genes conferring resistance to Pca have been cataloged. However, only limited genes have been mapped, and the chromosomal location of most remains undetermined. The goals of this study were to detect the chromosomal locations of 13 cataloged Pc genes and one uncharacterized but highly effective resistance gene and to identify functions related to them. We used an A. sativa L. nested association mapping population comprising 14 biparental F_2:3 families, derived from crosses between a donor carrying Pca resistance and the Pca susceptible variety "Swan." A total of 2,356 F_2:3 lines were phenotyped for response to pathotypes of Pca, from which the final AsNAM population of 707 individuals were selected. Based on DArT-Seq genotype data 15,940 high-quality single nucleotide polymorphisms were identified. Using the IBD mixed model, eight resistance QTLs to Pca with varying phenotypic variance were identified. The locations of four previously mapped genes were confirmed (Pc38, chr7D; Pc45, chr2D; Pc46, chr3D; Pc50, chr3D), and two genes were mapped for the first time (Pc36, chr1C; Pc70, chr5D). Resistance QTLs from the highly resistant Ensiler variety were also identified for the first time. The results revealed that some families had a single dominant gene controlling resistance, while others had more complex resistance. Several genes were linked or allelic (Pc13, Pc46, and Pc50 on chr3D; Pc36 and Pc60 on chr 1C; Pc38 and Pc64 on chr 7D). A total of 31 putative genes belonging to eight protein families related with disease resistance were identified in detected QTL regions.

Key message: BS-D275, a new locus on chromosome arm 2DS, is genetically independent of WFZP-2D and controls branched spike architecture in common wheat (Triticum aestivum). Branched spikes enhance wheat yield potential by increasing grain number. We identified the locus BS-D275 for spike branching in the winter wheat line Dong 275 and mapped it to chromosome arm 2DS using a recombinant inbred line (RIL) population derived from the cross of Dong 275 (branched spikes) × Zhongmai 175 (standard spikes). Across multiple field trials, spike branching and awn length segregated as polygenic, unlinked traits. Bulk segregant RNA-seq (BSR-Seq) of leaf and inflorescence samples, integrated with molecular markers, delimited BS-D275 to a 1.52-cM interval spanning 829 kb (84.03-84.86 Mb) in the Chinese Spring telomere-to-telomere reference genome. Diagnostic markers and sequence comparison positioned BS-D275 11 Mb distal to the spike-branching locus WFZP-2D (73.09 Mb), confirming their independence. The interval contains 10 inflorescence-specific candidate genes. CSIAAS2DG0371200/TraesCS2D02G133500, encoding a GTPase-activating protein, carries a Dong 275-specific 4-bp frameshift and is highly expressed in spikes, making it the most likely candidate for BS-D275. Parallel BSR-Seq of awned versus tip-awned bulks mapped the awn suppressor to the B1 locus (CSIAAS5AG1310200/TraesCS5A02G542800) on chromosome arm 5AL, demonstrating that awn development and spike branching are under separate genetic control. WFZP-2D represses awn development while BS-D275 does not, which provides evidence that BS-D275 is most likely a novel regulator of spike branching. Diagnostic markers for BS-D275 will accelerate marker-assisted selection for high-yielding, branched-spike wheat.

Key message: A missense SNP G → A mutation in the z-type thioredoxin-coding gene CsTRX z (CsDVL) reveals its pivotal regulatory function in chloroplast development, chlorophyll homeostasis, and low-temperature-sensitive photosynthetic regulation, with direct implications for targeted genetic improvement in breeding programs. Thioredoxins (TRXs), pivotal redox regulators modulating protein function, are essential for plant stress adaptation, development, and growth. While extensively characterized in model species (e.g., Arabidopsis, rice), their roles in vegetable crops remain underexplored. Here, we report a missense SNP (G → A) in the z-type thioredoxin CsTRX z (CsDVL), identified via ethyl methanesulfonate (EMS) mutagenesis, as the causal variant underlying the Dominant Virescent Leaf phenotype in cucumber (Cucumis sativus). The mutant PSM004 exhibits transient yellow-green cotyledons at seedling emergence, reverting to wild-type pigmentation during later growth stages. Genetic and cytological analyses confirmed that the Dominant Virescent Leaf (DVL) locus perturbs chloroplast ultrastructure, chlorophyll biosynthesis, and photosynthetic efficiency. Positional cloning delimited DVL to a 75.9-Kb region on chromosome 6, with allelic diversity analysis pinpointing a G → A substitution in the fourth exon of CsTRX z as the causative mutation. Transcriptomic profiling revealed that this missense SNP reprograms expression of chloroplast-localized genes governing chlorophyll metabolism, redox homeostasis, carbohydrate flux, and photosynthetic machinery. Physiological assays further demonstrated thermosensitivity in PSM004, with low-temperature treatment (20 °C/15 °C) inducing reversible chlorosis in developing leaves. Our findings elucidate CsTRX z's conserved yet distinct role in chloroplast biogenesis beyond model systems and establish its utility as a genetic target for enhancing stress resilience and photosynthetic performance in cucumber breeding programs.

Key message: Substantial improvements in genomic prediction accuracy for rice gene bank accessions were achieved by incorporating SNPs of low call rate identified in a recently published rice pan-genome. Introduction of useful genetic variation to breeding populations is a key factor in achieving genetic gain in crop breeding. However, identifying donors from genetic diversity stored in gene banks requires extensive phenotyping, which is not feasible for many traits of interest. Genomic prediction (GP) of phenotypic values has been proposed to overcome this phenotyping bottleneck. A key challenge for GP is the identification of appropriate markers representative of genetic variation causal for phenotypes. Here we report on utilizing single nucleotide polymorphisms (SNPs) from the core and dispensable genomes of a rice pan-genome resource comprising 16 reference sequences. Using a published pan-genome graph, we identified SNPs within structural variations of the dispensable genome. In this SNP set, SNPs of low call rate (CR) were common. Presence-absence variation (PAV) of these SNPs was associated with subpopulation structure, indicating that SNP absence reflects on underlying sequence PAV rather than being solely due to technical errors in SNP detection. To incorporate these SNPs in GP models, we employed modified encoding, retaining information of PAV and nucleotide variation by one-hot encoding (OHE). Adding these to SNP matrices increased prediction accuracies of GP for some traits and subpopulations. Improvements could largely be attributed to the inclusion of PAV. Our results show that the traditional approach of applying strict CR filters to SNPs located in the dispensable genome disregards potentially valuable genetic information not in linkage with SNPs of high CR. The proposed strategy provides a straightforward way to enhance GP performance in rice gene bank accessions.