Molecular Breeding最新文献

The presence of cadmium (Cd) in rice poses a significant health risk to consumers, highlighting the urgency of breeding rice varieties with low Cd accumulation. To identify genetic resources and potential genes for developing such rice varieties, a comprehensive genome-wide association study (GWAS) was conducted on 158 rice varieties, which tested between 2021 and 2023 in low cadmium accumulation testing framework, to identify candidate genes associated with cadmium content in brown rice. Based on their parental origin and genetic population structure analysis, we categorized these 158 varieties into four subgroups: Luohong, lcd1, intermediate and early indica series. Specifically, the four subgroups of low cadmium varieties were breeded based on OsNramp5 mutants Luohong 3A/4A, lcd1, Lian 1S and Shaoxiang 100, respectively. GWAS analysis identified sixteen loci significantly associated with cadmium content, twelve of which showed consistent associations across multiple environments, these loci were mapped to chromosomes 1, 2, 5, 7, 11, and 12, suggesting their potential for further fine mapping and functional validation. Through gene function annotation analysis, candidate genes related to cadmium content in these loci were identified, including Os05 g0382200, Os07 g0232800 (OsZIP8), Os07 g0232900 (OsHMA3), Os07 g0257200 (OsNramp5), Os07 g0258400 (OsNramp1), Os12 g0512100, Os12 g0512700, and Os12 g0514000. These genes are implicated in the absorption, transport, and accumulation of heavy metals, particularly cadmium. Haplotype analysis of key genes OsZIP8, OsHMA3, OsNramp5, and OsNramp1 identified specific low-cadmium dominant haplotypes. Notably, OsHMA3-Hap2 (GC), OsNramp5-Hap1 (DEL), and OsNramp1-Hap1 (DEL) were associated with Luohong-origin varieties, while OsHMA3-Hap1 (AC), OsNramp5-Hap2 (AA), and OsNramp1-Hap2 (GGG) were linked to lcd1-origin varieties. Overall, this study illustrated the genetic basis for breeding low-cadmium rice varieties and provided candidate loci to develop molecular markers to enhance food safety through reduced heavy metal content.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01575-z.

Cowpea is an important multipurpose legume crop that used for food, feed and vegetable worldwide. Developing the high yield cultivars is the first target in cowpea breeding, however, the genetic basis of this complex trait is not yet well understood. To discover the genetic architecture of cowpea yield, a total of 215 cowpea landraces collected from Zhejiang Province were evaluated for four yield-related traits including branch number per plant (BNP), grain number per pod (GNP), pod length (PL), and pod number per plant (PNP). By resequencing this diversity panel, total of 3,880,169 high-confidence single nucleotide polymorphisms (SNPs) were identified, population structure analysis showed that these cowpea landraces were classified into four subpopulations and the subpopulation division was highly related to the pod length and pod-type. Through conducting a GWAS on the four traits, 24 genomic regions significantly associated with cowpea yield were detected and haplotype analysis showed the favorable genotypes of each locus has stronger genetic effect on the yield-related traits. Based on the cowpea G98 reference genome, six predicated genes (VuG9806G022730, VuG9809G015960, VuG9801G022820, VuG9801G008990, VuG9801G016500, VuG9807G013020) were identified as the likely candidate genes for BNP_6.2, BNP_9.1, GNP_1.1, PL_1.1, PNP_1.2 and PNP_7.1, respectively, which involving in multiple pathways such as auxin response and regulation, cell expansion and ovary development. These results will facilitate the molecular breeding of high yield cultivars in cowpea and benefit for improving the global food security and the nutritional structure of human diets.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01585-x.

Broccoli (Brassica oleracea L. var. italica) is a globally important vegetable due to its rich nutrients as well as its anti-cancer effect. China is the world's largest producer and exporter of broccoli. However, since the research on commercial breeding of broccoli in China started relatively late, the level of genetic breeding in our country lags behind with more than 80% seeds imported. To assist broccoli breeding with molecular markers, we re-sequenced 41 representative broccoli inbred lines at high coverage depth and identified a total of 1,348,968 SNPs. From these SNPs, a genotyping-in-thousand by sequencing (GT-seq) SNP panel composed of 700 evenly distributed high-quality SNPs was developed. We assessed the genetic diversity, population structure, and kinship of 114 B. oleracea varieties bred in different institutions including broccolis, cabbages, cauliflowers and kales with this SNP panel, and found that the genetic diversity of these varieties was somewhat limited, with an average heterozygosity of 18.35% and an average Polymorphic Information Content (PIC) of 0.26. Population structure analysis divided the varieties into two main groups, consistent with the origin from two independent domestication events. The SNP panel was also employed to screen individuals with high background recovery rates in backcross breeding. Furthermore, the SNP panel was used to test seed purity of parental inbred lines and F1 hybrids, which could expedite the entry of hybrid seeds into the market. Overall, the developed GT-seq SNP panel is a valuable tool for various aspects of B. oleracea breeding and genetics studies.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01586-w.

Stripe rust is prevalent in the wheat-growing region of southwestern China. Frequent changes in stripe rust pathogen virulence in this region lead to a rapid loss of disease resistance among wheat varieties. However, Chinese wheat landrace Yizhanghongkemai (YZHK) has exhibited adult-plant stripe rust resistance for more than one decade in a disease nursery in southwestern China. To elucidate the underlying genetic basis, quantitative trait loci (QTLs) for adult-plant stripe rust resistance in YZHK were analyzed using an inclusive composite interval mapping method. Six QTLs for adult-plant stripe rust resistance were detected on chromosomes 1BL, 2BL, 3DS, 5BL, 5DL, and 7DS in multiple environments. Notably, QYrYZHK.saas-1B, QYrYZHK.saas-2B and QYrCY.saas-5D were likely new disease resistance loci. By comparing the effects of QTL alleles on yield and its related components in field trials in which stripe rust was severe and effectively controlled, we determined that three QTLs significantly decreased yield losses due to stripe rust, among which the QTLs on chromosomes 1BL and 7DS were from YZHK, whereas the QTL on chromosome 5DL was from the other parent Chuanyu 12. These QTLs represent elite genetic resources for developing wheat varieties with adult-plant stripe rust resistance in the wheat-growing region of southwestern China.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01583-z.

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.