Molecular Breeding最新文献

Capsaicinoids and their low pungent analogs are the important compounds to determine quality of chili pepper fruit in food industrial and medical purposes. Our previous screening for chili pepper bio-resources has shown that the pungent accession 'Charapita' (CH) (Capsicum chinense) has a unique composition with a higher capsinoid content. This study aimed to identify the mutation responsible for the high capsinoid content in CH. QTL analysis was performed using F₂ population between Red Habanero (RH) and CH, and it detected a major QTL on chromosome 3. Further genetic analysis showed that the QTL was narrowed down to approximately 400 kb region, which includes VAMT (vanillin aminotransferase). Allelism test demonstrated that CH possesses a leaky vamt allele. The sequencing analysis revealed that CH-type vamt allele has a unique amino acid substitution (G373E) due to a SNP in exon 15. CH-type vamt decreased pungency by 50%, and increased capsinoid content about three times compared with RH-type. We designated the CH-type allele as vamt ^L3. There was no difference in the expression levels of VAMT or other capsaicinoid biosynthetic genes between RH and CH. The vanillylamine synthesis activity was evaluated with crude extract from placental tissue. It showed that the activity in CH was 30 times less compared with RH. Given that the enzyme activity significantly decreased without transcriptional change, G373E likely reduces VAMT activity, conferring the characteristic composition of capsaicinoids and capsinoids. The novel vamt allele (vamt ^L3) will contribute to manipulate pungency level and capsinoid content in chili pepper breeding.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01595-9.

Panicle-related traits are important factors affecting the final yield of foxtail millet, and it is imperative to detect their underlying genetic basis. In this study, we constructed a genetic linkage map using the F₂ population crossed by Changsheng07 and Donggu218, two foxtail millet lines with significant differences in panicle-related traits. The genetic linkage map included 159 SSR markers and 37 Indel markers, covering 1545.5 cM, with average distance of 7.89 cM between adjacent markers. Quantitative trait loci (QTL) mapping was conducted by combining the genetic linkage map and the phenotypic data of nine panicle-related traits in F_2:3 families, and a total of 22 QTL were identified, with phenotypic variation explained (PVE) of 0.06-50.14%. Among them, the increased effect alleles of 16 QTL were derived from the parent Changsheng07, and seven QTL (qMPL3.1, qMPL5, qMPW2, qSD5, qTGW5.1, qTGW5.2 and qGL5) were major QTL, which explained the phenotypic variation of 11.41%, 12.78%, 13.75%, 34.81%, 50.14%, 40.28% and 11.32%, respectively. Moreover, 13 of 22 QTL formed four QTL clusters. These results will lay a foundation for the cloning and functional analysis of candidate genes involved in panicle development, and provide a theoretical basis for breeding high yield varieties through molecular marker-assisted selection in foxtail millet.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01594-w.

Rapeseed pods are prone to dehiscence, resulting in yield loss at maturity. In the present study, we investigated the shatter resistance index (SRI) of 280 doubled haploid (DH) lines derived from a cross between ZS11 (susceptible line) and R11 (resistant line). Based on the phenotypic data obtained from four environments and a high-density genetic map, a significant QTL (qSRI.A06) for shatter resistance on A06 chromosome were stably detected. This locus explained 4.80% - 15.00% of the phenotypic variation and the peak position covered a 664 Kb region. The effect of qSRI.A06 was verified in BC₃F₂ and BC₃F₃ populations and delimited in a 90.8 Kb region comprising 11 genes. Out of these genes, a differencially expressed gene, BnaA06g27900D, was identified to be involved in cell wall development by comparative transcriptome analysis. Regional association revealed four SNP/Indel variations in the promoter associated with pod shattering resistance. The highest Indels A06-41975887 showed suggestive association with SRI (p = 8.80E-06) with a TG allele variation. The stable locus qSRI.A06 and the candidate gene BnaA06g27900D will be helpful for understanding the resistance mechanism and improving shatter resistance in rapeseed.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01590-0.

Cytoplasmic male sterility (CMS) caused by mitochondrial genome alterations in flowering plants plays a crucial role in hybrid breeding systems. In pear (Pyrus spp.), pollenless phenotypes have been consistently observed in progeny. However, the genetic basis and inheritance mechanisms of male sterility in pears remain poorly understood. To investigate the inheritance mode, we performed segregation analysis in four F₁ populations derived from crosses using a cultivar carrying CMS-type cytoplasm as the maternal parent. The observed male sterility segregation ratios confirmed a maternal inheritance pattern consistent with the CMS model and suggested differential effects of nuclear fertility restorer genes from various pollen parents. We analyzed whole-genome sequencing data from four pear accessions, identifying an 860 bp mitochondrial DNA sequence associated with male-sterile individuals. This sequence was located near cox3 and apt8, commonly co-located with CMS loci in other plant species. Within this region, we identified orf206, a chimeric open reading frame composed of 113 bp from nad3 in Pyrus betulifolia and 403 bp from atp9-1 of Malus × domestica. The predicted protein encoded by orf206 contained three transmembrane domains, which are typical features of CMS-associated proteins. Our results demonstrate that male sterility in pears is maternally inherited and support orf206 as a strong candidate gene for CMS induction. Furthermore, we developed an InDel marker (CBpMtid03 and CBpMtid07) targeting the CMS-specific mitochondrial sequence enabling the efficient identification of CMS individuals in breeding programs. These findings provide insights into the molecular mechanisms underlying pollen sterility in pears and facilitate marker-assisted selection in pear breeding.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01591-z.

Soybean [Glycine max (L.) Merr.] seed morphology markedly influences yield, productivity, and nutritional value. However, assessing quantitative traits remains challenging due to their complexity and strong genotype-by-environment interactions. In this study, a high-throughput phenotyping (HTP) system was used to evaluate 13 image-based traits and a hundred-seed weight in a soybean mutant diversity pool (MDP) comprising 192 genotypes. All traits exhibited significant variations within the mutant diversity pool across multiple environments. Correlation analysis revealed strong positive and negative correlations among the traits regarding seed size, shape, color, and weight. Genome-wide association studies (GWAS) were conducted using 37,249 single nucleotide polymorphisms (SNPs) generated through genotype-by-sequencing (GBS) to uncover the genetic architecture of seed-related traits. The image-based GWAS identified 79 significant quantitative trait nucleotides (QTNs) that were simultaneously detected under all environments. Notably, five novel pleiotropic QTNs were consistently mapped to chromosomes 7, 10, 15, 18, and 20, each associated with a specific candidate gene. These genes exhibited marked expression differences during the seed developmental stages between the wild-type cultivar and its mutant. The HTP-integrated GBS demonstrates a powerful approach for precise trait dissection and genomic selection. These findings provide critical insights into the genetic architecture underlying desirable seed morphology and offer valuable tools for advancing precision soybean breeding.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01584-y.

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.