Molecular Breeding最新文献

Ovule number sets the upper limit on seed yield in plants, yet the molecular control of ovule initiation remains largely unknown. Here, we characterised a spontaneous ovuleless (ol) mutant that bears round leaves, produces seed-empty fruits and completely lacks ovule primordia. Genetic analysis of 512 F₂ plants showed that the phenotype is governed by a single nuclear locus. Whole-genome resequencing of mutant and wild-type DNA bulks revealed a strong Euclidean-distance peak at the distal end of chromosome 2. Six newly developed InDel markers delimited ol to a 1.8 Mb interval, but suppressed recombination within this region prevented further reduction of the interval size. Leveraging the Tnt1 insertional background, we detected two retrotransposon insertions unique to the mutant: one in exon 8 of Csa2G377920, encoding a lectin receptor-like kinase, and the other in the promoter of Csa2G403160, encoding a DOG1-domain bZIP transcription factor. Quantitative RT-PCR showed that transcripts from both genes are nearly abolished in ol mutants. Spatial and temporal profiling indicated that Csa2G403160 is strongly expressed in female buds during ovule primordium initiation and is rapidly induced by the synthetic cytokinin CPPU, whereas Csa2G377920 exhibits weak, constitutive expression and is cytokinin-insensitive. Collectively, phenotypic, genetic and expression evidence pinpoint Csa2G403160 as the most likely causal gene underlying the ovuleless phenotype and highlight cytokinin-responsive bZIP signalling as a previously unrecognised layer in cucumber ovule development.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01606-9.

Plant architecture and yield potential of wheat are significantly influenced by plant height (PH). In the present study, a diversity panel consisting of 199 Pakistani wheat cultivars was evaluated for PH in three environments, and a genome-wide association study (GWAS) was conducted to identify loci associated with reduced height. GWAS identified 19 loci associated with reduced height, of which 12 were consistently identified in all environments. Allelic variations were analyzed in the diversity panel for five Rht genes, including Rht-B1, Rht-D1, Rht13, Rht25, and Rht26, using diagnostic KASP markers. Furthermore, a KASP marker was developed to identify the dwarfing allele Rht-B1p in wheat. The GA-insensitive dwarfing allele Rht-B1b allelic frequency was pre-dominant (69.6%), followed by the GA-sensitive Rht26 mutant allele (58.5%). Five dwarfing alleles of Rht25, including Rht25c, Rht25d, and Rht25e were rarely present in the cultivars, with frequencies of 1.5%, 1%, and 0.5%, respectively. The use of alternate dwarfing alleles to reduce PH can increase the genetic base of wheat cultivars by reducing selection pressure on the Rht-B1b/Rht-D1b haplotype and can lead to the development of wheat cultivars with improved characteristics such as reduced lodging risk, increased resource allocation to grain, improved harvest efficiency, enhanced crop stability, and adaptability.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01600-1.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a major threat to global wheat production. Developing resistant wheat varieties is a crucial objective in wheat breeding programs. The Chinese common wheat cultivar Gaoyuan813 (GY813) has exhibited excellent resistance to Pst under field conditions for several years. The objective of this study was to identify quantitative trait loci (QTLs) associated with stripe rust resistance using a recombinant inbred line (RIL) population derived from a cross between Gaoyuan813 and the susceptible variety Fukuho. The RILs were evaluated for stripe rust resistance in four field environments with a mixture of Chinese prevalent Pst races (CYR32, CYR33, CYR34, Zhong4, and HY46) and in a growth chamber with race CYR34 and genotyped using the Wheat55K single nucleotide polymorphism array. Five QTLs for stripe rust resistances were mapped to chromosomes 1BL (2), 2AS (2), and 7DS (1), explaining 4.37%-25.44% of the phenotypic variance. QYrsicau-2AS.1 and QYrsicau-7DS were stably detected across all field environments, whereas QYrsicau-1BL.2 was only detected in the growth chamber test. QYrsicau-1BL.1 and QYrsicau-7DS may correspond to the known resistance genes Yr29 and Yr18, respectively, while QYrsicau-1BL.2 and QYrsicau-2AS.2 are likely novel. Additive effects were observed for the combination of QYrsicau-1BL.1, QYrsicau-2AS.1, and QYrsicau-7DS. KASP markers linked to QYrsicau-1BL.2 (KASP_AX-109878201) and QYrsicau-2AS.1 (KASP_AX-110981112) were developed and validated to facilitate the breeding use of genes for wheat improvement.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01616-7.

Unraveling the genetic architecture of nitrogen response of development is critical for improving wheat productivity while reducing nitrogen inputs. In this study, hyperspectral imaging (HSI) was applied to wheat grains obtained from nitrogen-deficient and normal conditions, combined with genome-wide association studies (GWAS), to investigate the nitrogen response of development in a diverse wheat panel. The 1,792 i-traits were acquired via hyperspectral imaging system, which reflect detailed phenotypic assessments of wheat development, capturing subtle variations in nitrogen response. A total of 3,556 significant loci and 3,648 candidate genes were identified. Key candidate genes involved in nitrogen uptake and utilization were identified by integrating agronomic traits with i-traits, including TaARE1-7A, TaPTR9-7B, TaNAR2.1, and Rht-B1. This approach underscores the potential of combining HSI on grains with GWAS to dissect complex traits like nitrogen response, offering valuable genetic insights for breeding nitrogen-efficient wheat varieties and enhancing sustainability in crop production.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01609-6.

Drought is one of the main factors restricting the increase of maize yield. Many genes respond to drought at seedlings have been cloned but less were effective in field. So, more work of understanding the genetic basis of drought response in field experiment need to be done due to its complexity. Herein, we constructed an association panel to carry on genomic wide association mapping for seven important traits under well-watered at whole period and drought at flowering stage. Then, 117 SNPs were identified, 50 SNPs of which were co-located among these traits or treatments or environments, including 50 SNPs identified under drought and 67 SNPs under well-watered. After merging the co-located SNPs, 90 SNPs were obtained. Combining the RNA-seq data of maize inbred line B73 under drought stressed from the public database, 31 differential expressed genes around the associated SNP were considered as drought responsive genes. Through protein interaction analysis and Gene Ontology enrichment analysis, it was shown that these genes are involved in regulating biological processes such as the tricarboxylic acid cycle, glycolysis, cell mitosis, and flowering signaling. And as the aggregation of related favorable allele genes improves the drought tolerance of materials. These results provide some candidate genes for in-depth analyzing the drought resistance mechanism when the drought happened at flowering stage during field experiment.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01599-5.

To enhance agricultural productivity and resilience in the face of changing climatic conditions, innovative strategies over traditional breeding methods are essential to shorten the breeding cycle for developing new climate-smart crop varieties, thereby supporting food security for a growing global population. Speed breeding (SB) is a promising cutting-edge approach to decrease crop life cycle, enabling accumulation of desirable traits in plants, thereby increasing crop yield and resilience to biotic and abiotic stresses. SB integrates advanced technologies such as marker-assisted selection, genetic engineering, genome editing, and high-throughput plant phenotyping to expedite desired traits incorporation to the plant more precisely. SB technology allows plant breeders to improve selection accuracy, and boost genetic gain, thereby accelerating breeding process for improvement and development of new crop varieties. However, it requires sophisticated infrastructure, intensive management, cost and skilled personnel. This review provides updates of SB, covering its prerequisites, benefits and constraints in applications. Additionally, the synergy of SB with transgenic breeding, high-throughput phenotyping and genome editing for crop improvement is critically discussed. In summary, SB offers a potent strategy for plant breeders to mitigate climate change impacts and ensure food security through efficient agricultural research and production technologies.

The release of the rice reference genome marked the beginning of a genomic era for crops. Over the past decades, the improvements in genome sequencing and assembly techniques, coupled with the continuous decrease in cost, had revolutionized crop research and breeding. In this review, by text mining the literatures published from 2000 to 2024, we summarize the traits, tissues, and methods prioritized by crop scientists during this period. These analyses reveal profound influence of genomic approaches across all the stages of crop research and breeding, and propose a 4D roadmap of crop research, which are decoding, discovery, design and delivery, representing four steps from crop genome sequencing (decoding) to breeding (delivery). The results also highlight a strong bias of crops and traits in the current studies. Finally, a dramatic increase in the frequency of keywords related to artificial intelligence (AI) indicate wider and deeper AI applications in crop science, forecasting the imminent AI era for crops.

Cotton hybrids offer significant advantages, the application of male sterile lines in cotton hybrid breeding can reduce the cost of artificial castration and ensure hybrid seed purity. Pollen and anther development are a crucial aspect of plant fertility, sporopollenin synthesis provides the major component of the outer walls in pollen (exines) for preserving pollen grains activity, mutations in the genes involved in sporopollenin synthesis affect pollen development and fertility formation. The differentially expressed genes (DEGs) between the developing anthers of genic male sterile mutant (ms1) and its genetic background Coker 312 were identified, the genes related to pollen exine and anther cutin biosynthesis were screened from the DEGs. GhCYP704B1 (Gh_D12G2768) was the DEGs with a significantly down-regulated expression level in ms1 anthers, kept very low expression level in ms1 developing anthers. At the same time, we also screened 20 homologies of GhCYP704B1 from DEGs data, and the results showed that only GhCYP704B1 was predominantly expressed in cotton anthers, while other homologies did not show significant expression changes. We used VIGS technology the expression level of GhCYP704B1 in cotton C312, resulting in disrupted callose formation during the tetrad formation of microspore development, partial defect of the pollen exine, weakened pollen activity, low pollen germination rate, and poor plant fertility. The expression levels of genes related to pollen exine and anther cutin synthesis changed significantly, the composition and content of cutin monomers in cotton anthers were significantly reduced in GhCYP704B1-silenced lines. Abnormalities in callose caused blockage of sporopollenin synthesis and failure to synthesize the pollen exine properly. The findings indicate that GhCYP704B1 affects cotton fertility and is involved in pollen exine biosynthesis, thus providing a candidate gene for creating new male sterile lines in G. hirsutum.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01608-7.

The identification of germplasm with high phosphorus efficiency is helpful to the genetic improvement of wheat. In this study, a doubled haploid (DH) population was used to investigate the traits related to phosphorus efficiency and map relevant loci under different conditions. On this basis, the association panel was used to verify mapping results. The results showed that shoot phosphorus concentration (SPC) and shoot phosphorus uptake per plant (SPUP) decreased, while shoot phosphorus utilization efficiency (SPUE) increased under low phosphorus. Correlation analysis showed that seedling biomass and root diameter could provide reference for identification of phosphorus efficiency. Twenty-one stable loci related to phosphorus efficiency were detected by linkage analysis. Among these, 11 loci including QRC-4D, QSpue.7A.2, and QSpup.7A.2 haven't been reported yet. The physical interval of QRC-4D was detected by three seedling phosphorus efficiency indexes, along with five seedling morphological indexes and five adult agronomic traits, which explained phenotypic variation up to 31.18%. In the association panel, QSpue.7A.2 associated with SPUE was also detected by genome-wide association study. Gene analysis revealed two candidate genes related to phosphorus within QRC-4D and QSpue.7A.2. These results provide valuable insights into genetic improvement and gene mining aimed at improving high phosphorus efficiency in wheat.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01596-8.