Molecular Breeding最新文献

The genetic trade-offs among complex traits are often witnessed in rice, however, very little is known about the contributing genes and mechanisms to exploit in breeding programmes. Here, we aimed to understand the genetic trade-offs among disease resistance, quality, and yield traits employing genome-wide association mapping. In all, 78 common marker-trait associations (MTAs) were identified for the targeted traits. In addition, five pleiotropic MTAs, 17 tightly linked MTAs, and two pleiotropic and tightly linked MTAs were detected for various trait combinations. The majority of MTA clusters were observed for quality traits (15 clusters) followed by the combined yield and quality traits (5 clusters) while only one cluster was found for combined yield and disease resistance traits. Further, the prediction of candidate genes controlling MTA clusters by exploiting the publicly available rice genome databases, revealed D-type cyclin 3;1 and Xyloglucan endotransglucosylase were found to be responsible for controlling grain size traits. We found no significant large linkage drag blocks with major MTAs for the targeted traits indicating that the indica rice genotypes have fewer trade-offs compared to japonica. The current study provides deeper insights into the genetic trade-offs among complex traits in rice, aiding in the meticulous planning of future breeding strategies.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01578-w.

Northern Corn Leaf Blight (NCLB), caused by the fungal pathogen Setosphaeria turcica, is a destructive disease on maize. Identification of resistance quantitative trait loci (QTLs) or genes is crucial for breeding maize varieties with durable resistance to NCLB. Although a lot of resistance QTLs against NCLB have been isolated, only a few have been fine-mapped to date. Here, a BC₁F₁ population was developed from a cross between the resistance line CIMBL75 and the susceptible line Liao3162. This population was inoculated with mixed conidia of six S. turcica races. Through five field trials, five resistance QTLs against NCLB were identified in this BC₁F₁ population. One of them, qNCLB3.04 on bin3.04, was repeatedly detected across all five trials. It explained 4.8-9.3% of phenotypic variation. Furthermore, the qNCLB3.04 locus was narrowed down to a 5.053 Mb region by using a progeny-based sequential fine-mapping strategy. Hence, qNCLB3.04 holds significant potential for improving maize broad-spectrum resistance against NCLB.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01581-1.

Apple trees are frequently subjected to varying degrees of salt stress. HYL1, a key protein involved in miRNA biosynthesis, has been shown to play critical roles in plant responses to cold, drought, and pathogen infection. However, the specific function of MdHYL1 in mediating salt-alkali stress tolerance in apple remains unknown. In this study, we demonstrated that overexpression of MdHYL1 in M9-T337 rootstocks significantly enhanced salt-alkali stress tolerance, including improved growth performance, reduced Na⁺/K⁺ ratio, decreased membrane damage, enhanced photosynthetic, and antioxidant capacity, which significantly impairs their growth, fruit quality, and yield. Moreover, scions grafted onto MdHYL1 OE rootstocks displayed superior saline-alkali stress tolerance compared to those grafted onto M9-T337 rootstocks. Taken together, our findings highlight MdHYL1 as a promising candidate gene for improving saline-alkali stress tolerance in fruit trees through biotechnological approaches.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01579-9.

Heading date (HD) is a critical agronomic trait that influences wheat's adaptation to environmental conditions and plays a pivotal role in yield stability. In this study, an early-heading mutant jg1489 was identified following γ-ray irradiation of the wild type (WT) wheat variety Jing411. This mutant headed 2-3 days earlier than the WT, with no significant differences in other yield-related traits. Bulked Segregant Analysis (BSA), genetic linkage analysis of the F₂ population from a cross between the WT and mutant, and phenotypic validation in F_2:3 lines were used to finely map the HD gene to a 12.4-Mb region on chromosome 5B. Transcriptome analysis of developing spikes from both WT and jg1489 at three key developmental stages revealed that differentially expressed genes (DEGs) were significantly enriched in pathways related to photosynthesis and photosynthesis-antenna proteins, suggesting a potential role in photosynthetic regulation. Within the mapped region, six high-probability candidate genes were identified based on sequence variation and expression patterns. Functional annotation, supported by studies of homologs in other species, highlighted three genes encoding serine proteases, bromodomain-containing protein, and UTP-glucose-1-phosphate uridylyltransferase as the most likely regulators of HD. These findings provide valuable insights into the genetic regulation of HD in wheat and support the development of new wheat varieties with optimized heading times.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01580-2.

Breeding varieties that are highly resistant to Alternaria leaf blight is crucial to enable carrot growers to drastically reduce their use of synthetic fungicides. Some sources of resistance have been identified in recent years, but in limited number and the genetic control as well as the screening for resistance remain complex and tedious. Flavonoid compounds have been reported to be involved in plant resistance to biotic or abiotic stresses. Their level of variation could therefore be a way of assisting screening activities for resistance. The aim of the study is to validate this link throughout the carrot growth cycle, in various environments and across a wide genetic diversity. A kinetic study showed that three flavonoid compounds are differentially accumulated between resistant and susceptible accessions as early as the 2-leaf stage and all along the plant development. Moreover, this differential is maintained throughout the potential infectious process in different environments. The analysis of a large range of accessions representing a very wide diversity of geographical origins, genetic structures, breeders and varietal types validates the link between resistance and the content in flavonoid compounds. These results open up extremely interesting prospects for the development of a marker-assisted early selection tool that would facilitate the screening and introgression of resistances into elite material, a complex task due to the polygenic control of resistance and biennial nature of the crop.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01573-1.

Rice hull color (HC) is crucial for improving the mechanization efficiency of hybrid rice seed production. However, the genetic resources for hull color currently available for practical production are limited, highlighting an urgent need to explore natural variations that can be utilized in breeding. In this study, we conducted a genome-wide association study (GWAS) on the hull color of 301 rice germplasm resources and identified a significant quantitative trait locus (QTL) qHC3.2 on chromosome 3. In this QTL, we identified a 7.3 kb natural structural variation (SV) in the Golden Hull 1 (GH1) promoter region, which suppresses the expression of GH1 and leads to the golden hull phenotype. We have screened seven germplasm resources that contain this natural variation. By introducing GH1™ into U1S, the hull color of U1S™ remains stable and is unaffected by drying time, demonstrating its potential value for breeding applications. Our study provides valuable natural variations and germplasm resources for the mechanized production of hybrid rice.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01569-x.

Taigu genic male-sterile wheat, containing the dominant gene male sterile (Ms) 2, shows completely male-sterility in different genetic background and under various environments. The development of Aibai wheat with tightly linked Ms2 and Reduced height (Rht)-D1c, offers possibility for identifying the male-sterile plants by investigation of reduced plant height. However, due to the extreme dwarfism of Aibai wheat caused by Rht-D1c, it inhabits a shadowed microenvironment caused by its fertile sibling plants. This results in delayed maturation of sterile plant progeny. In order to develop a novel germplasm with new visible marker for sorting male sterile plants conferred by Ms2, a binary vector containing Bar, Ms2, Rht-D1b, and DsRed driven by the aleurone-specific promoter Ltp2 was constructed and introduced into the wheat Fielder using Agrobacterium-mediated transformation in this study. After investigation of the fertility, plant height and seed fluorescence of positive transgenic wheat plants, a line exhibited semi-dwarf male sterility, which could be reliably identified by the aleurone-specifically expressed red fluorescence in seeds, serving as a genetically stable reporter. Therefore, this study provides a novel male-sterile wheat that offers a powerful tool for hybrid seed production and facilitates genetic improvement in wheat through recurrent selection.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01571-3.

Cowpea is an important grain legume crop and a source of vegetarian protein. C-152, a popular and widely adapted variety of cowpea, became susceptible to major cowpea diseases, viz., bacterial leaf blight (BLB) and cowpea mosaic virus (CpMV). Thus, in the current investigation, we have introgressed BLB and CpMV resistance from V-16 and V-57817, respectively, to the C-152 variety. A marker assisted simultaneous and stepwise backcross breeding scheme was used to recover an improved version of C-152 with resistance to BLB and CpMV diseases. Foreground (CISP markers VuMt401 and VuMt397 for BLB and SSR markers MA15 and MA80 for CpMV) and background selections were practiced using gene-specific and recurrent genome specific (72 markers) polymorphic markers. Two independent BC₂F₄ lines from each cross possessing blb-1 and cowpea mosaic resistance gene with maximum genome recovery of the C-152 were inter-crossed to derive an inter-cross (IC) F₄ population. Among the 10 promising ICF₄ progenies, the line MC 17-2 (KBC-12), showing high yielding with resistance to BLB and CpMV, was selected. The superiority of the cowpea line MC 17-2 was evident in terms of a yield advantage of 8.68 to 28.68%, 9.30-47.00%, 1.10-8.10% over different check varieties in the initial varietal trial, advanced varietal trial (AVT)-I, and AVT-II, respectively. Further, the multi-location evaluation of KBC-12 (MC 17-2) with the check KBC-9 covering zones 5 and 6 of Karnataka reconfirmed the high-yielding potential and stability of KBC-12 across tested environments, as evident from AMMI and GGE biplots. Thus, the promising cowpea line KBC-12 was released for commercial cultivation in zones 5 and 6 in southern India during 2024 and can also be used as a donor (IC652010) of BLB and CpMV resistance. Our current study is one such examples that revealed the power of marker-assisted selection to deliver improved cultivars from lab to farmers' field.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01570-4.

Walnut (Juglans regia L.), an important woody oil plant, is cultivated globally and has a prominent position in the world's major nuts. Heterozygosity enriches plant genetic diversity by providing a wider array of gene combinations, significantly enhancing their adaptability to the environment and consequently improving their survival ability. In this study, we found that the heterozygosity rate was significantly correlated with 21 traits. Heterogeneity rate showed the strongest positive correlation with yield and nutrition, while it showed the most significant negative correlation with tree height and precocity. Among these, 13 traits showed positive correlations, the remaining 8 traits exhibited negative correlations. We conducted an in-depth study on the characteristics of walnut whole-genome heterozygosity. By using the GWAS based on the heterozygosity rate, we successfully identified 11 significant loci and 4 candidate genes. In the analysis of local heterozygosity rate by GWAS, it was found that 63.8% exhibited trans-acting and 36.2% exhibited cis-acting. In addition, with the help of genomic residual heterozygotes, we enriched functional genes from 44 Pfam families related to growth regulation and development. Finally, it is worth mentioning that during the process of walnut improvement, we observed an increase in the heterozygosity rate of genes related to the flowering time. It is speculated that a higher level of whole-genome heterozygosity can enhance the environmental adaptability of plants and improve their growth performance. The results of this study may provide assistance for optimizing the breeding strategies of walnuts.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01572-2.