Theoretical and Applied Genetics最新文献

Key message: Sparse testcrossing with 3-5 testers enhances genetic gain in hybrid breeding programs, offering a practical balance of simple testcross designs, resource efficiency, and increased prediction accuracy for general combining ability. Sparse testcrossing is an effective strategy for increasing both short- and long-term genetic gain in hybrid breeding programs. Maize hybrid breeding programs aim to develop new hybrid varieties by crossing genetically distinct parents from different heterotic pools, exploiting heterosis for improved performance. The programs typically consist of two main components: population improvement and product development. The population improvement component aims to enhance the heterotic pools through reciprocal recurrent selection based on general combining ability (GCA). However, especially in the early stages of testing, evaluating large numbers of hybrid combinations to estimate GCA is impractical due to considerable logistical challenges and costs. Therefore, breeders often evaluate the initial population of selection candidates using only a single tester to narrow down the candidate pool before further evaluation. Using a single tester, however, may not adequately represent the heterotic pool, leading to inaccurate GCA estimates and suboptimal selection decisions. To address this, we propose sparse testcrossing for early-stage testing, where subsets of candidate genotypes are testcrossed with different testers, connected through a genomic relationship matrix. We conducted stochastic simulations to compare various sparse testcrossing designs with a conventional testcross strategy using a single tester over 15 cycles of reciprocal recurrent genomic selection. Our results show that using 3-5 testers, sparsely distributed among full-sibs, sparse testcrossing offers breeders a practical balance between simple testcross designs, resource efficiency, and increased prediction accuracy for GCA, ultimately resulting in increased rates of genetic gain.

The content and composition of fatty acids are crucial determinants of soybean nutritional quality. In this study, we conducted an expression genome-wide association analysis (eGWAS) using 298 soybean germplasm accessions. We identified 904,984 high-quality SNP markers (MAF > 0.02, missing data ≤ 10%). Thirty-three association signals were identified that correlated with to the expression levels of very long chain fatty acid (VLCFA) genes. Integrating KEGG pathway enrichment analysis with gene haplotype analysis, we identified GmLACS11 as the candidate gene that potentially involved in regulating long-chain fatty acid biosynthesis. We performed subcellular localization, bioinformatics analysis, and functional validation of the GmLACS11 gene. The fatty acid content was measured following GmLACS11 gene expression in Saccharomyces cerevisiae eukaryotic expression, Arabidopsis thaliana, and in soybean overexpression and knockout lines. The results demonstrated that both overexpression and knockout of GmLACS11 gene altered soybean fatty acid composition. Overexpression significantly increased the levels of the polyunsaturated fatty acids, linoleic acid and linolenic acid, and a corresponding rise in the total fatty acid content was observed. These findings provide insights into the regulation of soybean very long chain fatty acids biosynthesis and the genetic mechanisms underlying soybean fatty acids composition.

Anthracnose is an important fungal disease in cucurbits, caused by the pathogen Colletotrichum orbiculare, which negatively affects all the aboveground parts of the plant. Race 2 anthracnose causes severe economic damage in watermelon. The objective of the study was to identify race 2 anthracnose resistance QTL in a biparental mapping population and association mapping panel. For the F₂ biparental population (N = 188), resistant and susceptible parents were PI 189225 (C. amarus) and 'New Hampshire Midget' (C. lanatus), respectively. The association mapping panel consisted of 1,008 watermelon germplasm accessions (C. amarus (N = 72), C. lanatus (N = 894), and C. mucosospermus (N = 42)). The biparental mapping population identified a significant QTL for race 2 anthracnose resistance, Qar2-3 (LOD = 4.53), on chromosome 3 from the resistant parent, PI 189225. In the association mapping panel, MLM and BLINK models identified a significant marker S06_9279285 and S08_ 28493121 (LOD > 5) on chromosomes 6, Qar2-6, and 8, Qar2-8, respectively, conferring resistance to anthracnose race 2. Three receptor kinase genes (CaUC03G056690, CaUC03G056730, and CaUC03G056740) were close to the Qar2-3. Similarly, leucine-rich receptor-like protein kinase family protein (ClCG06G007520) and serine/threonine protein kinase (ClCG08G016080) genes were close to the Qar2-6 and Qar2-8, respectively. Inconsistent results on QTL locations between the biparental and association mapping populations could be due to various factors including selected germplasm, minor allele frequency, linkage disequilibrium (LD), LD decay, and genotyping. Future research should focus on identifying and understanding the roles of LRR-RLKs genes in governing resistance.

Soil salinization severely limits plant growth and development, posing a significant threat to agriculture. NAC transcription factors are widely involved in the regulation of various abiotic stresses. In this study, we discovered that SlNAC63 responds to both saline-alkali and jasmonic acid (JA) signaling and enhances saline-alkali tolerance in tomato (Solanum lycopersicum L.) by improving the reactive oxygen species (ROS) scavenging capacity. The experiments of Y1H, EMSA, and ChIP-qPCR confirmed that SlNAC63 directly targets and regulates the expression of tomato SlAOS1 and superoxide dismutase SlSOD4. This, in turn, promotes JA biosynthesis and enhances ROS scavenging ability, thereby positively regulating saline-alkali tolerance in tomato. Phenotypic analysis demonstrated that overexpressing SlAOS1 indeed increases JA accumulation, while overexpressing SlSOD4 significantly improves ROS scavenging under saline-alkali stress. Through Y2H, pull-down, and Co-IP assays, we found that SlNAC63 interacts with SlbHLH71. Furthermore, SlbHLH71 enhances the regulatory effects of SlNAC63 on SlAOS1 and SlSOD4 by interacting with SlNAC63 to strengthen its binding affinity to the promoters of SlAOS1 and SlSOD4, thereby promoting JA accumulation and ROS scavenging, which ultimately strengthens saline-alkali tolerance in tomato. This study unveils the central role of the SlNAC63-SlbHLH71 module in the regulation of saline-alkali stress and clarifies the molecular mechanism by which this module participates in the response of tomato to saline-alkali stress through the regulation of JA accumulation and ROS scavenging.

The European potato germplasm originated from a few founding genotypes, and its narrow genetic base has since been broadened through introgressions from wild relatives. We combined pedigree records and genome-wide SNP data to trace the origin, spread, and contributing ancestors of modern breeding introgressions in Europe. We first used a curated pedigree database to identify the Major Contributing Ancestors (MCAs) of 1209 varieties from the European Common Catalogue, revealing influential cultivars such as Katahdin, Saskia, and Agria as the top contributors to the modern European gene pool. Building on this framework, we developed a modified MCA approach that uses SNP alleles to trace the spread of haplotypes that were introduced into the European germplasm after 1945; two of which now occur in half of European varieties. Using the pedigree database to find the origin of these modern introgressions, we traced key contributions from S. vernei, S. demissum, and S. tuberosum Group Andigena clone CPC 1673. We observed multiple distinct haplotypes of the R3a/b late blight resistance introgression on chromosome 11. Additionally, we generated a genome assembly of S. demissum to validate a single sub-genome origin of the R3a/b introgression. We also traced a putatively starch-associated introgression derived from S. vernei. Our framework links historical breeding records with genomic data, revealing the legacy of modern introgression breeding in the European germplasm.

Developing and deploying multi-use naked barley varieties that accumulate lower levels of deoxynivalenol (DON) resulting from Fusarium head blight (FHB) disease could help farmers mitigate economic risks and expand market possibilities. Previous work established that a substantial amount of DON in covered barley accumulates in the hull and can be removed by pearling. We studied a diverse panel of 244 naked barley lines to determine if there is a genetic variation for the distribution of DON in Fusarium-infected spikes. We evaluated the panel genotyped with a 50K Barley SNP array for disease severity, toxin accumulation, and other agronomic traits in two FHB disease nurseries from 2020 to 2021. Harvested naked barley spikes separated into hull and kernel fractions revealed that 11.92-70.02% of the total toxins were localized in the hull. Single-SNP and haplotype-based genome-wide association studies (GWAS) were carried out using mixed linear models. Based on the single-SNP GWAS, 132 marker-trait associations, localized into 13 quantitative trait loci, were identified for all the traits except FHB severity. Haplotype-based GWAS found two haplotype-trait associations each for DON in hull and plant height, three for DON in rachis, and five for heading date. Notably, markers and haplotypes associated with later heading were also linked to higher levels of the toxin in the hull but not the kernel. Moderate-to-high predictive abilities suggest that genomic selection could be used to develop improved naked barley cultivars with a lower risk of DON contamination.

Estimating recombination fractions is crucial for constructing genetic linkage maps and understanding the inheritance patterns of crop genome in breeding populations. Traditional methods, such as the maximum likelihood method, rely on iterative algorithms to estimate recombination fractions in $F_2$ populations, which can be computationally intensive. While most existing methods focus on recombination fractions in $F_2$ , recombination fractions in later generations ( $F_t$ for $t>2$ ) is also important for capturing the increasing resolution of genetic maps over generations. In this study, we introduced a Pearson correlation method for estimating recombination fractions in $F_t$ for $t\ge 2$ . This is the first study to demonstrate that the Pearson correlation between marker alleles of different loci can be effectively used to estimate the recombination fractions between markers in advanced generations. This method is straightforward, allowing researchers to quickly and efficiently compute recombination fractions, offering a significant speed advantage without compromising estimating accuracy. We evaluated the performance of the new method by comparing it with the expectation-maximization (EM) algorithm across $F_2$ , $F_3$ , and $F_4$ populations using a rice dataset. The results show that the Pearson correlation method is both reliable and computationally efficient. In addition, we construct a genetic linkage map across generations utilizing the genetic distance calculated from the correlation converted recombination fractions. We observed map expansion, where the estimated genetic map length increases in later generations, reflecting improved resolution and detection of recombination events under finite marker density and sample size. This approach holds significant potential for broader applications in linkage mapping, quantitative trait loci (QTL) analysis, and design of breeding programs.

Key message: This study demonstrates that the US cotton landrace collection provides a rich resource of genetic resources for improved agronomic and fiber quality performance for future cotton improvement. The Gossypium hirsutum L. landrace collection (n ~ 2500), maintained by the US cotton germplasm collection in College Station, TX, USA, has been underutilized in cotton cultivar development programs. Underutilization is due to: (1) the common photoperiod sensitive growth habit of landraces that requires short day length to stimulate reproductive growth and (2) a lack of relevant phenotypic data for traits of interest in cotton production. In this study, the entire G. hirsutum landrace collection was first field evaluated in the Southeastern United States for photoperiod insensitivity. A total of 186 naturally occurring day-neutral accessions were identified and self-pollinated over 2-3 years to maintain heterogeneity and assemble a total of 216 accessions (including some component lines). Second, the 216 day-neutral accessions, along with eight elite, upland breeding lines and cultivars, were evaluated over 2 years for per se agronomic and fiber quality performance in replicated field trials under rainfed and irrigated conditions. On average, day-neutral landraces produced lint yield and lint percent lower than elite checks while they did not differ from elite checks for seed protein, seed oil, and fiber quality properties. Several day-neutral landraces were identified with desirable lint yield and fiber quality under rainfed and/or irrigated conditions. In total, this large evaluation of day-neutral landrace per se agronomic and fiber quality performance provides a much-needed resource to facilitate their efficient selection as breeding parents for cotton improvement.

Key message: The wheat adult-plant powdery mildew resistance gene Pm62 was introgressed through a T2DS·2VL translocation, fine-mapped to a narrowed region on chromosome 2VL, and its impact on yield-related traits was characterized. Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), threatens global wheat production. Adult‑plant resistance (APR) genes from wheat relatives remain crucial for its control. The APR gene Pm62 was previously introduced into wheat via the T2BS·2 V#5L translocation from Dasypyrum villosum, while the susceptible T2DS·2 V#4L line NAU198 was also created. Here, we developed a Pm62-harboring T2DS·2 V#5L translocation line, NAU197, from DS2V#5(2D)/NAU0686 progeny and verified its chromosomal constitution using molecular cytogenetic approaches. Inoculation with Bgt isolate E09 demonstrated that both NAU197 and NAU198 were susceptible at the three-leaf stage; however, NAU197 displayed significant resistance after the five-leaf stage and achieved full resistance during elongation. Genetic analysis of NAU197/NAU198 F₁ and F₂ populations confirmed that Pm62 functions as a single dominant gene. Using 37 polymorphic markers on the 2VL arm, we mapped Pm62 in 233 F₂ plants to an interval flanked by InDel markers F30 (0.08 cM) and F79 (0.04 cM). Further screening of 2733 F₂ plants identified 11 recombinants within Pm62 interval, and eight newly developed markers delimited Pm62 to a ~ 0.6 Mb region between F86 and F108 in the D. villosum 91C43^DH reference genome. This region contains nine high‑confidence protein‑coding genes and five uncharacterized proteins, among which two C2‑domain genes and two chitinase genes are prime candidates. The new T2DS·2 V#5L translocation in wheat background NMZ167 showed no yield penalty. Our results establish an effective strategy for genetic mapping of alien genes and provide a valuable genetic resource and molecular tool for wheat breeding focused on disease resistance.