Molecular Breeding最新文献

In breeding programmes, accurate estimation of breeding values is crucial for selecting superior genotypes. Traditional methods rely on phenotypic observations and pedigree information to estimate variance components and heritability. However, pedigree errors can significantly affect the accuracy of these estimates, especially in long-lived perennial vines. This study evaluates the effect of pedigree errors on breeding value predictions in kiwiberry breeding and explores the benefits of using genomic selection. We applied Best Linear Unbiased Prediction (BLUP) to estimate breeding values for each genotype for a given trait. Four scenarios with varying degrees of alteration in pedigree-based relationship matrices were used to represent inaccurate relationships between genotypes. Pedigree-based breeding values were compared with genomic estimated breeding values for one vine-related and four fruit-related quantitative traits. The results showed that as the degree of altered population structure increased, the prediction accuracy of pedigree-based breeding values decreased. In contrast, genomic selection, which uses marker inheritance, maintained realised relationships between genotypes, making it a more robust method for predicting genetic merit. In kiwiberries, as in all species of the genus Actinidia, only female vines bear fruit. The genotypic merit of fruit-related traits in male genotypes can only be estimated indirectly. Marker-based predictions outperformed pedigree-based predictions, especially for genotypes without phenotypic observations, such as male siblings. This study reviewed the induced population structures and introduced genomic selection into the kiwiberry breeding programme. We demonstrated that genomic selection provides more accurate breeding values by capturing true genetic relationships and reducing the effects of misidentified relationships between individuals.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01552-6.

Covered barley (Hordeum vulgare) has historically been preferred for malting, as the husk in this plant protects the embryo during harvest and acts as a filter during brewing. Naked barley, which is typically used as food, has the potential to be used in brewing due to recent technical advances, but the grains contain higher levels of β-glucan and polyphenols, which are undesirable in brewing. Introducing the naked trait into brewing cultivars through crossing is time-consuming due to the need to eliminate these undesirable traits. In this study, we rapidly developed naked barley that is potentially suitable for malting by introducing targeted mutations into Nudum (NUD) using CRISPR/Cas9-mediated targeted mutagenesis. The doubled haploid line 'DH120366', which was used as the parental line, was derived from a cross between two covered malting barley cultivars. We generated CRISPR/Cas9-mediated targeted mutagenized barley harboring mutations in NUD via Agrobacterium tumefaciens-mediated transformation and confirmed the presence of mosaic mutations in one individual from among 16 T₀ transformants. We sowed T₁ grains exhibiting the naked trait and sequenced the NUD gene in these T₁ seedlings, identifying two types of mutations. Shotgun high-throughput whole-genome sequencing confirmed the absence of the transgene in at least one nud mutant line following k-mer-based analysis. Cultivation in a closed growth chamber revealed no significant differences in agronomic traits between the nud mutants and the wild type. This study demonstrates the feasibility of rapidly developing naked barley with potential use for malting and brewing by targeting only NUD via targeted mutagenesis.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01553-5.

Inter-specific hybridisation between natural populations within the genus Actinidia is a common phenomenon and has been used in breeding programmes. Hybridisation between species increases the diversity of breeding populations, incorporating new desirable traits into potential cultivars. We explored genomic prediction in Actinidia breeding, focusing on the closely related species Actinidia arguta and Actinidia melanandra. We investigated the potential of genomic selection by analysing four quantitative traits across intra-specific A. arguta crosses and inter-specific crosses between A. arguta and A. melanandra. The continuous distributions of the studied traits in both intra-specific and inter-specific crosses indicated a polygenic background. A linear mixed model approach was used, incorporating the factor of year of season and a marker-based relationship matrix instead of pedigree as a random effect. After evaluation, the best model was applied to assess variance components and heritability for each quantitative trait. Expanding beyond intra-specific crosses, predictive ability was calculated to investigate inter-specific cross effect. Considering predictive ability, this study explored the impacts of sample size and population structure. A reduction in sample size correlated with decreased predictive ability, while the influence of population structure was particularly pronounced in inter-specific crosses. Finally, the prediction accuracy of genomic estimated breeding values, for parental genotypes, revealed an inter-species effect on prediction confidence. Considering the imbalance in genotype numbers between intra- and inter-specific cross populations, this research highlights the difficulty of genomic prediction in hybrid populations. Understanding prediction accuracy in inter-species crossing designs provides valuable insights for optimising genomic selection.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01550-8.

Heterosis has been widely applied in crops production. Nonetheless, how to determine the favorable recombination of non-alleles remains elusive. Due to the uncertainty of genetic recombination, hybrids with strong heterosis tend to be selected empirically, by developing and testing a tremendous number of combinations. Here, we found some individuals in recombinant inbred lines (RILs, F₉) that were generated from hybrid F₁ (HRF₁) with heterosis performed transgressive segregation for yield in multiple environments. The result suggested that the formation of yield heterosis in hybrid was caused by the effective recombination of genes or QTLs. We performed multiple regression analysis (MRA) and redundancy analysis (RDA) using 11 traits measured in four environments. Of these traits, percentage of female flowers (PFF), fruit length (FL), fruit neck length (FNL), vine length (VL) and vine diameter (VD) contributed to increase yield. Moreover, the genes or QTL of yield contributor traits were identified by the molecular mapping strategy. We predicted a fl7.1 candidate gene that encoding a KIP1-like protein through correlation analysis between haplotype and fruit length phenotype. Based on the phenomenon some RILs individuals performed transgressive segregation and genetic theory, we proposed the model that the genetic sources of heterosis are contributed by combination of heterozygotic advantages and genetic recombination effects. Our work provides the theoretical basis for the pyramid of contributor genes or QTL for yield heterosis. This work also may facilitate Marker-assisted Selection for promote hybrid pyramid breeding and makes yield increasing more predictable in cucumber.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01551-7.

In peach, a long peduncle can help minimize mechanical damages/physical injuries in the fruit at harvest and can also be useful in postharvest handling and transportation. In view of genetically dissecting the peduncle length (PL) in peach, we have performed a Quantitative Trait Locus (QTL) mapping study for PL using a F₂ progeny of 117 individuals from the cross 'PI 91459 [NJ Weeping]' x 'Bounty' (WxBy). The progeny was phenotyped for three years (2011, 2012 and 2014) and the QTL mapping analysis was performed using four methods: Kruskall-Wallis, Interval Mapping, Multiple QTL Mapping and Genome-Wide Composite Interval Mapping. QTL analysis led to the identification of 9 QTLs distributed on linkage groups (LG) 1, 2, 4, 5, 6 and 7. A stable QTL was identified on LG6 (22,978,897 to 24,666,094 bp) and explained up to 63% of the phenotypic variance. Within the genetic interval of the stable QTL on LG6 potential candidate genes with functional annotation encompassing cellular expansion, hormone regulation, transcriptional regulation, developmental processes such as meristem development, and responses to environmental cues were found. The results reported in this study represent the first insight into the genetic basis of PL and a step forward towards the introduction of novel traits in peach commercial breeding in order to minimize the problems related to mechanical damage/injuries to peach fruits that commonly might occur during at harvest and post-harvest processes.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01547-3.

Gray leaf spot (GLS) is one of the most damaging foliar diseases in maize. In previous research, we identified the ZmCPK39 gene, which confers resistance to GLS. This study demonstrates the utility of ZmCPK39 in breeding resistant maize varieties. Two parental lines of Zhengdan958 (the most widely cultivated hybrid in China), Chang7-2 and Zheng58, were selected for resistance improvement. These lines were crossed with Y32, a donor line high resistance to GLS, followed by six rounds of backcrossing to their respective recurrent parents. Foreground selection was performed in each generation to detect ZmCPK39, while background selection was conducted in the BC₆F₁ generations using a Maize 6 K DNA chip. The converted lines, Chang7-2 ^ZmCPK39 and Zheng58 ^ZmCPK39 , with a recovery rate of 94.67-96.48%, were crossed to produce the improved hybrid Zhengdan958 ^ZmCPK39 . This hybrid exhibited enhanced GLS resistance and an 11.95% higher yield under severe disease stress, while maintaining comparable yield performance under normal growth conditions relative to the original Zhengdan958. This study highlights the breeding potential of ZmCPK39 for improving GLS resistance in maize.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01549-1.

Maize, a primary global food crop, is crucial for food security. In recent years, climatic and other abiotic stresses have led to frequent global droughts. Ascorbate peroxidase (APX) plays a vital role in the ascorbate-glutathione cycle. Under drought stress, APX effectively scavenges reactive oxygen species (ROS) produced by plants and maintains the normal growth and development of organisms. This study successfully amplified APX-related genes, and the ZmAPX2 gene was screened using expression analysis. pCAMBIA3301-ZmAPX2-Bar and pCXB053-ZmAPX2-Bar plant expression vectors were constructed and transformed into the maize inbred line H120. Drought tolerance of plants was analyzed by phenotypic characteristics, physiological and biochemical indices in T₂ generation positive maize seedlings as well as agronomic traits at maturity. Results indicate that boosting APX2 gene expression enhances maize drought resistance by reducing ROS content. This research underpins the exploration of new drought-tolerant maize germplasm and resistance mechanisms.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01548-2.

Heterosis, a key technology in modern commercial maize breeding, is limited by the narrow genetic base which hinders breeders from developing superior hybrid varieties. By integrating big data and functional genomics technologies, it becomes possible to create new super maize inbred lines that resemble hybrid varieties through the aggregation of multiple QTL parental advantage loci. In this study, we utilized a combination of resequencing and field selfing selection methods to develop three pyramiding QTL lines (PQLs) (PQL4, 6, and 7), each containing 15, 12, and 12 QTL loci respectively. Among the three PQLs, PQL6 (266.78 cm/119.39 cm) demonstrated hybrid-like performance comparable to the hybrid (276.96 cm/127.02 cm) (P < 0.05). Testcross between PQL6 and the parental lines revealed that PQL6 had accumulated and fixed advanced parent alleles for superior traits in plant and ear height. The significant increase in PQL6 plant height primarily resulted from the aggregation of two major effective QTL (qEH2-1 and qEH8-1 on chromosomes 2 and 8), indicating that the aggregation of major effective QTL is a key selection indicator. Furthermore, PQL6 exhibited slow vegetative growth but experienced a rapid height increase during the reproductive stage, particularly in the 1-2 weeks before flowering, when its growth rate accelerated and surpassed that of the hybrid varieties. Our study explored the time period and key parameter indicators for molecular breeding of maize, providing a theoretical concept and practices for further complex multi-trait design and aggregation.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01546-4.

[This corrects the article DOI: 10.1007/s11032-024-01522-4.].

The stigma exsertion rate (SER) is a key factor in improving the outcrossing ability of cytoplasmic male sterility (CMS) lines in rice. In previous studies, we identified 18 SER-QTLs and developed some SER-QTL pyramiding lines (PLs). In this study, 4QL-1 and 4QL-2 were selected from these PLs and crossed with CMS maintainer lines H211B and H212B, respectively, to develop two new CMS maintainer lines, H221B and H222B, and their CMS lines H221A and H222A. The SER of H221B and H222B were 74.7% and 73.1%, respectively, reaching a high SER level. Compared with CMS maintainer lines, the CMS lines consistently exhibited higher SER, which may be related to the delayed flowering time of the CMS lines. Filed experiments showed that outcrossing seed-setting rates of H221A and H222A were significantly higher than those of the original CMS lines, which meets the requirements for hybrid rice seed production. These results confirm that SER is a key factor in enhancing rice outcrossing ability. Our findings demonstrate that pyramiding SER-QTLs is an effective strategy for improving rice SER and increasing outcrossing seed-setting rate.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01545-5.