Molecular Breeding最新文献

Late blight (LB), caused by Phytophthora infestans, is a destructive disease of the cultivated tomato, Solanum lycopersicum. Environmental concerns and pathogen resistance have propelled research towards developing host resistance. The current LB-resistant cultivars of tomato exhibit susceptibility under severe disease pressure, necessitating the identification, characterization, and incorporation of additional resistance genes into new tomato cultivars. Recently, we identified Solanum pimpinellifolium accession PI 270443 with strong resistance to LB and developed a RIL population from its cross with an LB-susceptible tomato breeding line. In the present study, we constructed a high-density genetic map of the RIL population, using 8,470 SNP markers set into 1,195 genomic bins, with a total genetic distance of 1232 cM and an average bin size of 1 cM. We identified 2 major adjoining LB-resistance QTLs on chromosome 10 and a few minor QTLs on chromosomes 1 and 12 of PI 270443. While one of the QTLs on chromosome 10 colocalized with the known LB-resistance gene Ph- 2 and a LB-resistance QTL previously identified in an F₂ population of the same cross, the present study allowed marker saturation of the region, fine mapping of the QTL, and identification of candidate resistance genes in the region. One of the 2 major QTLs on chromosome 10 and the 3 QTLs on chromosomes 1 and 12 were not previously reported in S. pimpinellifolium for LB resistance. These results will expedite transferring of LB resistance from PI 270443 into the tomato cultigen via MAS and discovering the underpinning LB-resistance genes in PI 270443.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01560-6.

Enhancing wheat yield and stress tolerance is a critical long-term objective for global food security. Historically, breeders selected genetic traits from wild wheat relatives for domesticated targets, such as non-shattering and free threshing characteristics, and developed the cultivated wheat. However, the genetic diversity of the cultivated wheat has become narrow after long-term domestication and conscious selection, which seriously limited the yield potential and stress tolerance. Therefore, using wild Triticeae species to broaden the gene pool is an ongoing task for wheat improvement. Psathyrostachy huashanica Keng ex P. C. Kuo (2n = 2x = 14, NsNs), a perennial species of the genus Psathyrostachys Nevski, is restrictively distributed in the Huashan Mountain region of Shaanxi province, China. P. huashanica exhibits considerable potential for wheat breeding due to its valuable agronomic traits such as early maturation, more tillers, abiotic tolerance, and biotic resistance. Over the past four decades, researchers have successfully crossed P. huashanica with common wheat and developed derivative lines with improved agronomic traits. Here, we summarized the morphology, genomic evolution, and derived wheat breeding lines with advanced agronomic characteristics inherited from P. huashanica. This review provides a useful guideline for future research on P. huashanica, and highlights its importance in wheat breeding.

Olive fruit weight is a crucial trait to consider in olive breeding programs due to its impact on final yield and its relevance for mechanical harvesting and fruit processing. Although environmental conditions influence this trait, fruit weight is primarily determined by genetic factors and exhibits a high degree of heritability in breeding progenies. Despite several studies identifying potential markers associated with fruit weight, these markers have not been validated. In this study, we analyzed 40 genetic markers linked to fruit weight using a dataset comprising 73 cultivars (including 33 newly sequenced varieties) and 10 wild olives with a wide range of phenotypic characteristics, spanning from very light (0.41 g) to very heavy fruits (8.57 g). By examining the phenotype distribution for each genotype of the newly sequenced varieties, we successfully validated 16 genetic markers. Additionally, machine learning tools demonstrated that 9 out of the 16 validated markers have a high predictive ability for fruit weight. As a result, our work provides, for the first time, a set of 9 well-validated genetic markers suitable for use in marker-assisted selection during the early stages of olive breeding programs.

Root is an important tissue to absorb water and nutrients from soil in plant and root architecture is one of critical traits influencing grain yield in crop. However, the genetic basis of root architecture remains unclear. In the present study, we identified a wild rice (Oryza nivara) introgression line Ra33 with longer seedling root length compared with the recipient parent 9311, an indica variety. Observation of longitudinal sections of root showed that the meristem length of Ra33 was significantly longer than that of 9311. Using an F₂ secondary segregating population derived from a cross between introgression line Ra33 and the recipient parent 9311, we detected a major QTL for root length at early seedling stage, qROL1, between the molecular markers M3 and M5 on chromosome 1, and the O. nivara-derived allele at qROL1 increased root length under the background of 9311. In addition, the near-isogenic line NIL-ROL1 showed a significant increase in root length compared with the recipient parent 9311, further demonstrating the genetic effect of qROL1. And then, a total of 159 recombinant individuals were screened from 3355 F₂ individuals and the QTL qROL1 was narrowed down to an approximate 78 kb interval between markers M4 and RM3, including 12 predicted genes. Further sequence comparison and expression analysis of the predicted genes in the fine-mapping region indicated that eight genes might be the interesting candidates of qROL1. The findings will provide new clues to reveal the genetic basis of root length and genetic resources for root architecture improvement in rice.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01564-2.

Ms and Ms2 are restorer-of-fertility loci in onion (Allium cepa L.); additionally, Ms2 is responsible for unstable male fertility in some accessions. Although a candidate gene was previously reported for the Ms locus, the gene responsible for the Ms2 locus remains unidentified. A 12.5 Mb genomic region harboring the Ms2 locus was initially obtained from onion whole genome sequences using two flanking markers to identify candidates. This region was further delimited to 3.19 Mb via fine mapping using 12 recombinants and 11 additional markers. A gene coding for a pentatricopeptide repeat (PPR) protein was identified within the 3.19 Mb region and designated AcPPR876. Phylogenetic analysis showed that AcPPR876 and four homologs belonged to the Rf-like PPR gene family. Polymorphic sequences between male fertile (MF) and male sterile (MS) AcPPR876 alleles were concentrated in the 5' region of the gene. Among them, a 446 bp insertion was identified at the putative promoter region of the MF allele. Although overall AcPPR876 transcription levels were very low, transcription levels of the MF allele were generally higher than those of the MS allele. A simple PCR marker was developed using the 446 bp insertion to perform Ms2 locus genotyping in the diverse onion germplasm. Although the dominant Ms2 allele was not found in any of the 250 domestic breeding lines, 29 out of 108 exotic accessions were shown to contain the dominant Ms2 alleles. Overall, the AcPPR876 gene is proposed as a strong candidate for the Ms2 locus.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01561-5.

Plant height is a crucial agronomic trait in wheat, regulated by multiple genes, and significantly influences plant architecture and wheat yield. In this study, a novel dwarf mutant, designated as m097, was developed and characterized through the treatment of seeds from the common wheat cultivar Jinmai47 with ethyl methanesulfonate (EMS). Microscopic analysis revealed that the dwarf phenotype was attributed to a reduction in the longitudinal cell size of the stem. Similar to the wild type, m097 exhibited sensitivity to exogenous gibberellic acid (GA). Genetic analysis indicated that the reduced plant height in m097 was regulated by a semi-dominant dwarfing gene, Rht_m097. Through bulk segregant analysis (BSA) utilizing the wheat 660K SNP array, Rht_m097 was mapped and confined to a region of approximately 2.58 Mb on chromosome arm 4BS, encompassing 16 high-confidence annotated genes. In addition, transcriptome sequencing (RNA-seq) was conducted on the first internode below the panicle of JM47 and m097 at the jointing stage, leading to the identification of two potential candidate genes exhibiting differential expression. Furthermore, the analysis of gene ontology and metabolic pathways from RNA-seq data indicated that the down-regulated differentially expressed genes (DEGs) in m097 were biologically classified as regulating actin cortical patch organization and assembly. Concurrently, it was observed that the up-regulated DEGs were significantly enriched in various phytohormone metabolic pathways, including those involved in indole-3-acetic acid (IAA) biosynthesis, jasmonic acid biosynthesis, and gibberellin signaling. Overall, this study provides a novel genetic resource for the breeding of dwarf wheat and establishes a foundation for subsequent gene cloning.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01558-0.

Amylose content and resistant starch (RS) are of great importance due to their multiple functionalities in the food and pharmaceutical industries and their benefits for human health. However, breeding high-amylose maize remains challenging because of the trade-off between amylose content and yield loss. Here, we report targeted mutagenesis of the key domains of starch synthases and branching enzyme including SSIIa, SSIII and SBEIIb via a CRISPR-Cas9 technology; this generated 15, 21, and 14 novel alleles, respectively, in the maize inbred line LH244. Except for ssIII mutants, the ssIIa and sbeIIb mutants had significantly greater apparent amylose content (AAC) and RS content compared with wild-type kernels. Although most mutants had reduced hundred-kernel weight (HKW) relative to wild-type plants, some mutants had only a small HKW reduction. Investigation of six representative mutants revealed that mutants of ssIIa and sbeIIb with higher AAC and RS content were accompanied with reduced starch content viscosity, increased content of reducing sugars and soluble sugars, and yet no apparent trade-off with agronomic traits. These findings offer a promising path for high-amylose maize breeding, accelerating the development of germplasms with enhanced RS content for the benefit of both global health and industry.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01559-z.

Take-all disease, caused by the fungal pathogen Gaeumannomyces tritici, severely impacts the growth and grain yield of wheat. Identifying loci associated with disease resistance can be achieved through molecular methods, along with data on morphological traits and disease severity. This study analyzed 100 bread wheat genotypes using molecular markers (SSR, IRAP technique, and translocation wheat-rye) and agronomical traits to pinpoint loci related to resistance to take-all disease. In this research, we propose a new approach using TOPSIS method for identifying ideal genotypes with resistance to take-all disease and the best in point of other agronomic traits. Genotypes were grouped based on agronomical traits (yield and its components) observed in the field, as well as root weight characteristics, root lignin content, and disease severity. These groupings effectively distinguished between resistant and sensitive genotypes. Stepwise regression techniques unveiled significant loci linked to disease resistance and agronomical traits. The presence of common loci suggests a potential pleiotropic nature of disease resistance. Molecular analysis exposed interactive loci contributing to trait variations and disease resistance, indicating gene-by-gene interactions. Using the IRAP technique, a locus from the LTR retrotransposon marker (LTR14) showed a strong correlation with take-all disease resistance and agronomic traits. This marker can serve as an informative and promising candidate for marker-assisted selection in wheat breeding programs. The TOPSIS method assisted in identifying genotypes showing high yield and resistance to take-all disease.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01554-4.

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most destructive diseases of rice worldwide. The utilization of host resistance (R) genes in rice breeding program is considered as the most economical, effective, environment-friendly strategy for rice blast control. The R gene Pigm, shows high, broad-spectrum and durable resistance to rice blast. Here, we report the successful integration of Pigm into Longke638S (LK638S), an elite thermo-sensitive genic male sterile (TGMS) line in hybrid rice production in China. The integration significantly enhanced the blast resistance of LK638S and the derived hybrid varieties demonstrated exceptional performance in both yield and blast resistance. The improved line Longzhen36S (LZ36S), which recovered 91.84% of the recurrent parent genome. LZ36S exhibited a high blast resistance frequency of 96.4% against 28 blast isolates. Furthermore, the LZ36S-derived hybrids exhibited enhanced resistance to both seedling and panicle blast compared to LK638S-derived hybrids carrying the heterozygous Pi2 gene, all without yield penalty. A total of ninety LK638S derived hybrid varieties have been state or provincial approved and certified with an annual promoting area exceed 964.0 thousand hectares. The LZ36S-derived hybrids can serve as improved versions with enhanced blast resistance, making them viable replacements for LK638S-derived hybrids in commercial production. Moreover, sixteen LZ36S-derived hybrid varieties, all possessing moderate (MR) or high (R) level blast resistance, along with excellent yield and grain quality, have been state or provincial approved and certificated. These LZ36S-derived hybrids show great potential for rapid commercialization, with promoting area of ~ 200 thousand hectares by 2023.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01555-3.

Tomato (Solanum lycopersicum L.) is a worldwide economically important vegetable crop, but the production is severely threatened by diseases and pests. Clarifying the presence of disease resistant genes in tomato germplasm is helpful for the development and deployment of resistant cultivars. In this study, 21 genes for resistance to 10 diseases were examined in a collection of 401 tomato accessions using gene-associated molecular markers. The results showed that the presence of the 21 genes in the 401 tomato accessions ranged from 0.2% to 66.1%. Frequencies (27.9-66.1%) of I-1, I-2, Sm, Tm-2a, and Ph-3 genes were higher than other genes, while frequencies (0.2-1.2%) of Ty-2, Ty-4, Mi-HT, I-3, and Tm-2 genes were very low. Based on the marker genotypes, 86.3% accessions carried at least one of disease resistance genes. Most (84.2%) Contemporary Processing F₁ (CPF) carried 4-8 genes and 74.1% Contemporary Fresh-market F₁ (CFF) carried 4-6 genes, while 87.4% Contemporary Processing Inbreds (CPI) carried 1-5 genes and 85.3% Contemporary Fresh-market Inbreds (CFI) carried 1-4 genes. Furthermore, the numbers of disease resistance genes were lower in Latin American Landrace (1-3), Vintage (1-3), and CFI (1-4) than in CFF (1-8), CPI (1-7), and CPF (2-10). Among multiple markers used for detection of the single gene, markers CAUTy4 and 18IY13 had the highest consistency (100%) of genotypes for the Ty-4 gene, followed by SM-InDel and InDel-FT-29 (94.0%) for the Sm gene, while markers AW910upF2R3, 20IY10, and TG0302 for detecting the Ty-2 gene had the lowest consistency (44.4%). Disease evaluation confirmed the accuracy of marker-assisted identification of corresponding genes except that the accessions carrying the Ty-1 gene uniquely detected by the CAPS1 marker were susceptible to tomato yellow leaf curl virus. The data obtained here provide valuable information for marker-assisted selection of these disease resistance genes and the use of these germplasm in tomato breeding and production.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01557-1.