Molecular Breeding最新文献

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.

In breeding programmes, accurate estimation of breeding values is crucial for selecting superior genotypes. Traditional methods rely on phenotypic observations and pedigree information to estimate variance components and heritability. However, pedigree errors can significantly affect the accuracy of these estimates, especially in long-lived perennial vines. This study evaluates the effect of pedigree errors on breeding value predictions in kiwiberry breeding and explores the benefits of using genomic selection. We applied Best Linear Unbiased Prediction (BLUP) to estimate breeding values for each genotype for a given trait. Four scenarios with varying degrees of alteration in pedigree-based relationship matrices were used to represent inaccurate relationships between genotypes. Pedigree-based breeding values were compared with genomic estimated breeding values for one vine-related and four fruit-related quantitative traits. The results showed that as the degree of altered population structure increased, the prediction accuracy of pedigree-based breeding values decreased. In contrast, genomic selection, which uses marker inheritance, maintained realised relationships between genotypes, making it a more robust method for predicting genetic merit. In kiwiberries, as in all species of the genus Actinidia, only female vines bear fruit. The genotypic merit of fruit-related traits in male genotypes can only be estimated indirectly. Marker-based predictions outperformed pedigree-based predictions, especially for genotypes without phenotypic observations, such as male siblings. This study reviewed the induced population structures and introduced genomic selection into the kiwiberry breeding programme. We demonstrated that genomic selection provides more accurate breeding values by capturing true genetic relationships and reducing the effects of misidentified relationships between individuals.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01552-6.

Covered barley (Hordeum vulgare) has historically been preferred for malting, as the husk in this plant protects the embryo during harvest and acts as a filter during brewing. Naked barley, which is typically used as food, has the potential to be used in brewing due to recent technical advances, but the grains contain higher levels of β-glucan and polyphenols, which are undesirable in brewing. Introducing the naked trait into brewing cultivars through crossing is time-consuming due to the need to eliminate these undesirable traits. In this study, we rapidly developed naked barley that is potentially suitable for malting by introducing targeted mutations into Nudum (NUD) using CRISPR/Cas9-mediated targeted mutagenesis. The doubled haploid line 'DH120366', which was used as the parental line, was derived from a cross between two covered malting barley cultivars. We generated CRISPR/Cas9-mediated targeted mutagenized barley harboring mutations in NUD via Agrobacterium tumefaciens-mediated transformation and confirmed the presence of mosaic mutations in one individual from among 16 T₀ transformants. We sowed T₁ grains exhibiting the naked trait and sequenced the NUD gene in these T₁ seedlings, identifying two types of mutations. Shotgun high-throughput whole-genome sequencing confirmed the absence of the transgene in at least one nud mutant line following k-mer-based analysis. Cultivation in a closed growth chamber revealed no significant differences in agronomic traits between the nud mutants and the wild type. This study demonstrates the feasibility of rapidly developing naked barley with potential use for malting and brewing by targeting only NUD via targeted mutagenesis.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01553-5.

Inter-specific hybridisation between natural populations within the genus Actinidia is a common phenomenon and has been used in breeding programmes. Hybridisation between species increases the diversity of breeding populations, incorporating new desirable traits into potential cultivars. We explored genomic prediction in Actinidia breeding, focusing on the closely related species Actinidia arguta and Actinidia melanandra. We investigated the potential of genomic selection by analysing four quantitative traits across intra-specific A. arguta crosses and inter-specific crosses between A. arguta and A. melanandra. The continuous distributions of the studied traits in both intra-specific and inter-specific crosses indicated a polygenic background. A linear mixed model approach was used, incorporating the factor of year of season and a marker-based relationship matrix instead of pedigree as a random effect. After evaluation, the best model was applied to assess variance components and heritability for each quantitative trait. Expanding beyond intra-specific crosses, predictive ability was calculated to investigate inter-specific cross effect. Considering predictive ability, this study explored the impacts of sample size and population structure. A reduction in sample size correlated with decreased predictive ability, while the influence of population structure was particularly pronounced in inter-specific crosses. Finally, the prediction accuracy of genomic estimated breeding values, for parental genotypes, revealed an inter-species effect on prediction confidence. Considering the imbalance in genotype numbers between intra- and inter-specific cross populations, this research highlights the difficulty of genomic prediction in hybrid populations. Understanding prediction accuracy in inter-species crossing designs provides valuable insights for optimising genomic selection.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01550-8.

Heterosis has been widely applied in crops production. Nonetheless, how to determine the favorable recombination of non-alleles remains elusive. Due to the uncertainty of genetic recombination, hybrids with strong heterosis tend to be selected empirically, by developing and testing a tremendous number of combinations. Here, we found some individuals in recombinant inbred lines (RILs, F₉) that were generated from hybrid F₁ (HRF₁) with heterosis performed transgressive segregation for yield in multiple environments. The result suggested that the formation of yield heterosis in hybrid was caused by the effective recombination of genes or QTLs. We performed multiple regression analysis (MRA) and redundancy analysis (RDA) using 11 traits measured in four environments. Of these traits, percentage of female flowers (PFF), fruit length (FL), fruit neck length (FNL), vine length (VL) and vine diameter (VD) contributed to increase yield. Moreover, the genes or QTL of yield contributor traits were identified by the molecular mapping strategy. We predicted a fl7.1 candidate gene that encoding a KIP1-like protein through correlation analysis between haplotype and fruit length phenotype. Based on the phenomenon some RILs individuals performed transgressive segregation and genetic theory, we proposed the model that the genetic sources of heterosis are contributed by combination of heterozygotic advantages and genetic recombination effects. Our work provides the theoretical basis for the pyramid of contributor genes or QTL for yield heterosis. This work also may facilitate Marker-assisted Selection for promote hybrid pyramid breeding and makes yield increasing more predictable in cucumber.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01551-7.