Molecular Breeding最新文献

Lack of seed dormancy (SD) often causes pre-harvest sprouting (PHS) or inadequate germination in cereal crops and seed production. This research aimed to integrate a dormancy (D) allele isolated from weedy rice at qSD12 into the genetic background of a restoration-of-fertility line (RFL) to mitigate the PHS and germination problems. A hybrid F₂ population was developed to map quantitative trait loci (QTLs) and model their epistatic and genotype-by-environment interactions. Twelve QTLs for flowering time (FT, 3), plant height (5) or SD (4) were identified. Of the 4 SD loci, qSD12 explained most of the phenotypic variance (R² = 0.34), and 2 (qSD3 & qSD6) have the D alleles from the RFL. qSD12 interacted with qSD3 or qSD7-2, with the presence of the D allele at qSD12 increasing the effects of the others, as well as the duration of seed storage at 24 or 40 ˚C for dormancy release. The F₂ plant-derived F₄ to F₆ lines were marker-assisted selected. The major effect of qSD12 on seed germination and on-panicle sprouting was confirmed with the F₄ and F₅ lines, respectively. A sample of F₂ plant-derived backcross (BC₁F₁) plants, which are heterozygous for 2-4 of the SD QTLs, was evaluated for agronomic traits and genotyped with an array of SNP markers. Recurrent backcrossing with the RFL and genomic selection are used to pyramid the D alleles from qSD12 and other locus/loci to develop new varieties and RF lines with improved resistance to PHS.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01623-8.

Snap bean (Phaseolus vulgaris L.), a nutrient-rich crop, is limited by Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV). To better understand the genetic basis of resistance, 376 snap bean accessions and 12 F₂ populations were screened with US-6 [pathogroup (PG)-VII], NL-8 (PG-III), or NL-3 (PG-VI) strains and genotyped for I, bc-1, and bc-3 loci using existing candidate gene-linked markers. Two Vps4 candidate genes associated with bc-u and bc-2 recessive loci were re-sequenced to identify novel mutations. Two major allelic groups of bc-u missense mutations were identified: (bc-u ^a = bc-u ^d = bc-u ^g) and (bc-u ^r ≤ bc-u ^s), each interacting differently with bc-1 and bc-2 to confer strain-specific resistance or susceptibility to NL-3 and US-6. New bc-2 ^{[IVT 7214]} and existing bc-2 ^[Robust] and bc-2 ^[UI-111] nonsense mutations exhibited functionally equivalent alleles, resulting in the same genetic effect across pathogroups. Twenty-six allelic combinations were found, 16 of which included the dominant I gene. Overall, 336 of 376 accessions carried I, of which 233 possessed I + RNase H-Like 1 ^C + bc-1 combination characteristic of host group (HG)-9 cultivars with restricted vein necrosis (VN) to NL-8. Importantly, 30 accessions possessed I + RNase H-Like 1 ^C + bc-1 + bc-u ^{a, d, or g}, conferring VN to NL-3 strain, characteristic of HG-10 cultivars. This panel provides a valuable resource of resistance diversity to BCMV and BCMNV, which can be used in breeding programs with the markers described. The bc-2 and bc-3 alleles, found in only one or two accessions, offer untapped resistance sources for snap bean.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01605-w.

Increasing global population, reduction of arable land, limitation of cultivable conditions due to global warming became a huge challenge for sustainable food production. There is a threat that the current plant breeding techniques may become obsolete in the face of these problems. Amid this challenges, novel technologies also presenting innovative tools to face these problems. In the era of precision genome editing, classical breeding strategies are considered to be time consuming, labor intensive and in near future, it will be considered as a rudimentary way of plant breeding when compared with techniques such as CRISPR/Cas9, Prime editing and base editing technologies. Even though these tools provide an accelerated approach for crop improvement, Targets for these tools must be carefully selected and utilized for more precise plant breeding programs. However, manipulating key traits such as flowering time can entail trade-offs, including altered resource allocation, reduced yield potential, or developmental constraints. Advances in sequencing technologies provide high-resolution insights into gene functions, enabling precise identification of targets to mitigate these trade-offs. Flowering time in model and cultivated crops has been extensively studied, with numerous homologs characterized for potential application. This review emphasizes flowering time as a major trait for crop improvement under current agro-dynamics, it highlights the associated trade-offs, and it discusses strategies which include gene editing, tissue-specific promoters, and conditional regulation to optimize flowering traits and enhance productivity in food, feed, fiber, and energy crops.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01620-x.

Enhancing rice yield per unit area is one of the most effective approaches to addressing the global food crisis. However, yield improvement is often accompanied by reduced stress resistance, making it imperative to balance productivity and resilience in current rice breeding efforts. Recent studies highlight phytohormone regulation as a promising strategy to achieve this balance. Ethylene, a hormone unique to plants, plays crucial roles in regulating rice growth, development, and stress responses, yet its role in coordinating grain yield and stress resistance remains unclear. In this study, we found that 1-aminocyclopropane-1-carboxylic acid synthase 3 (ACS3), a key rate-limiting enzyme in ethylene biosynthesis, was highly expressed in panicles and tiller buds, and that loss-of-function reduced ethylene levels. Furthermore, acs3 mutant significantly increased the number of productive panicles and grains per panicle, resulting in enhanced rice yield. Notably, the acs3 mutant exhibited enhanced yield per plant without significant reduction in stress resistance. These findings suggest that fine-tuning ethylene homeostasis via ACS3 rebalances growth and stress adaptation, offering a potential novel strategy for high-yield rice breeding with sustained stress tolerance.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01613-w.

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.