Molecular Breeding最新文献

Previous studies illustrated that two banana GA20 oxidase2 (MaGA20ox2) genes, Ma04g15900 and Ma08g32850, are implicated in controlling banana growth and development; however, the biological function of each gene remains unknown. Ma04g15900 protein (termed MaGA20ox2f in this article) is the closest homolog to the Rice SD1 (encoded by 'green revolution gene', OsSD1) in the banana genome. The expression of MaGA20ox2f is confined to leaves, peduncles, fruit peels, and pulp. Knockout of MaGA20ox2f by CRISPR/Cas9 led to late flowering and low-yielding phenotypes. The flowering time of ΔMaGA20ox2f #1 and ∆MaGA20ox2f #2 lines was delayed approximately by 61 and 58 days, respectively, while fruit yield decreased by 81.13% and 76.23% compared to wild type under normal conditions. The endogenous levels of downstream products of GA20 oxidase, GA15 and GA20, were significantly reduced in ∆MaGA20ox2f mutant shoots and fruits, but bioactive GA1 was only significantly reduced in the mutant fruits. Quantitative proteomics analysis identified 118 up-regulated proteins and 309 down-regulated proteins in both ΔMaGA20ox2f #1 and ∆MaGA20ox2f #2 lines, compared to wild type, with the down-regulated proteins primarily associated with photosynthesis, porphyrin and chlorophyll metabolism. The decreased chlorophyll contents in ΔMaGA20ox2f #1 and ∆MaGA20ox2f #2 lines corroborated the findings of the proteomics data. We propose that photosynthesis inhibition caused by lower chlorophyll contents in ΔMaGA20ox2f mutant leaves and GA1 deficiency in ΔMaGA20ox2f mutant fruits may be the two critical reasons contributing to the late flowering and low-yielding phenotypes of ΔMaGA20ox2f mutants.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01523-3.

This study investigated the potential of extended irradiation combined with immature embryo culture techniques to accelerate generation advancements in safflower (Carthamus tinctorius L.) breeding programs. We developed an efficient speed breeding method by applying light-emitting diodes (LEDs) that emit specific wavelengths, alongside the in vitro germination of immature embryos under controlled environmental conditions. The experimental design for light treatments followed a 2 × 4 completely randomized factorial design with four replications, incorporating two safflower varieties, Remzibey-05 and Dinçer, and four LED treatments (white, full-spectrum, red + blue + white, and control). A lighting regimen of 22 h of light and 2 h of darkness was applied for all the LED treatments, whereas the control received 18 h of light and 6 h of darkness. Additionally, the immature embryo culture experiment used a 2 × 2 × 4 factorial arrangement, assessing two safflower cultivars, two media types, and four embryo developmental stages, with three replications. The parameters evaluated included plant height, branch number, seed number per plant, seed number per head, time to flower initiation, time to 50% flowering, time to harvest, and germination percentage of in vitro cultured immature embryos at various developmental stages. The harvest time among the light treatments ranged from 50.62 to 73.12 days, with the shortest time achieved under the red + blue + white LED combination and the longest under the control treatment. The plant height, number of seeds per plant, and number of seeds per head were highest under the full-spectrum LED, control and red + blue + white LED combinations, respectively. Immature embryos rescued at 10 days post-pollination presented a 57% germination rate, with an increasing trend in germination as the number of days post-pollination increased. The germination rates did not significantly differ across varieties or hormone treatments. This study demonstrated the potential to achieve six generations per year by combining prolonged illumination with targeted LED lighting and immature embryo culture techniques. These findings provide valuable insights for optimizing safflower growth and development and advancing speed breeding in controlled environments.

Genomic selection-based breeding programs offer significant advantages over conventional phenotypic selection, particularly in accelerating genetic gains in plant breeding, as demonstrated by simulations focused on combating Fusarium head blight (FHB) in wheat. FHB resistance, a crucial trait, is challenging to breed for due to its quantitative inheritance and environmental influence, leading to slow progress using conventional breeding methods. Stochastic simulations in our study compared various breeding schemes, incorporating genomic selection (GS) and combining it with speed breeding, against conventional phenotypic selection. Two datasets were simulated, reflecting real-life genotypic data (MASBASIS) and a simulated wheat breeding program (EXAMPLE). Initially a 20-year burn-in phase using a conventional phenotypic selection method followed by a 20-year advancement phase with three GS-based breeding programs (GSF2F8, GSF8, and SpeedBreeding + GS) were evaluated alongside over a conventional phenotypic selection method. Results consistently showed significant increases in genetic gain with GS-based programs compared to phenotypic selection, irrespective of the selection strategies employed. Among the GS schemes, SpeedBreeding + GS consistently outperformed others, generating the highest genetic gains. This combination effectively minimized generation intervals within the breeding cycle, enhancing efficiency. This study underscores the advantages of genomic selection in accelerating breeding gains for wheat, particularly in combating FHB. By leveraging genomic information and innovative techniques like speed breeding, breeders can efficiently select for desired traits, significantly reducing testing time and costs associated with conventional phenotypic methods.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01527-z.

Pre-harvest sprouting (PHS) of wheat (Triticum aestivum L.) is one of the complex traits that result in rainfall-dependent reductions in grain production and quality worldwide. Breeding new varieties and germplasm with PHS resistance is of great importance to reduce this problem. However, research on markers and genes related to PHS resistance is limited, especially in marker-assisted selection (MAS) wheat breeding. To this end, we studied PHS resistance in recombinant inbred line (RIL) population and in 171 wheat germplasm accessions in different environments and genotyped using the wheat Infinium 50 K/660 K SNP array. Quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) identified 59 loci controlling PHS. Upon comparison with previously reported QTL affecting PHS, 16 were found to be new QTL, and the remaining 43 loci were co-localized with QTL from previous studies. We also pinpointed 12 candidate genes within these QTL intervals that share functional similarities with genes previously known to influence PHS resistance. In addition, we developed and validated two kompetitive allele-specific PCR (KASP) markers within the chromosome 7B region identified by linkage analysis. These QTL, candidate genes, and the KASP marker identified in this study have the potential to improve PHS resistance of wheat, and they may enhance our understanding of the genetic basis of PHS resistance, thus being useful for MAS breeding.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01526-0.

Citrus canker is a devastating disease caused by Xanthomonas citri subsp. citri (Xcc), which secretes the effector PthA4 into host plants to trigger transcription of the susceptibility gene CsLOB1, resulting in pustule formation. However, the molecular mechanism underlying CsLOB1-mediated susceptibility to Xcc remains elusive. This study identified CsCEL20 as a target gene positively regulated by CsLOB1. Cell expansion and cell wall degradation were observed in sweet orange leaves after Xcc infection. A total of 69 cellulase genes were retrieved within the Citrus sinensis genome, comprising 40 endoglucanase genes and 29 glucosidase genes. Transcriptomic analysis revealed that expression levels of CsCEL8, CsCEL9, CsCEL20, and CsCEL26 were induced by Xcc invasion in sweet orange leaves, but not in the resistant genotype Citron C-05. Among them, CsCEL20 exhibited the highest expression level, with an over 430-fold increase following Xcc infection. Additionally, RT-qPCR analysis confirmed that CsCEL20 expression was induced in susceptible genotypes (Sweet orange, Danna citron, Lemon) upon Xcc invasion, but not in resistant genotypes (Citron C-05, Aiguo citron, American citron). A Single-Nucleotide Polymorphism (SNP) at -423 bp was identified in the CEL20 promoters and exhibits a difference between eight susceptible citrus genotypes and three resistant ones. Moreover, CsCEL20 expression was upregulated in CsLOB1-overexpression transgenic lines compared to the wild type. Dual-luciferase reporter assays indicated that CsLOB1 can target the -505 bp to -168 bp region of CsCEL20 promoter to trans-activate its expression. These findings suggest that CsCEL20 may function as a candidate gene for citrus canker development and may be a promising target for biotechnological breeding of Xcc-resistant citrus genotypes.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01531-3.

Increasing planting density is one of the most important strategies for generating higher maize yields. Moderate leaf rolling decreases mutual shading of leaves and increases the photosynthesis of the population and hence increases the tolerance for high-density planting. Few genes that control leaf rolling in maize have been identified, however, and their applicability for breeding programs remains unclear. Here we identified a maize abaxially rolled leaf1 (arl1) mutant with extreme abaxially rolled leaves and found that the size of the bulliform cells within the adaxial leaf blade surface increased in the arl1 mutant. Bulk segregation analysis mapping in an F₂ population derived from a single cross between arl1 and inbred line Gui18421 with normal leaves identified the arl1 locus on chromosome 2. Sequential fine-mapping delimited the arl1 locus to a 233.56-kb genomic interval containing three candidate genes. Sequence alignment between arl1 and Gui18421 identified an 8-bp insertion in the coding region of Zm00001eb082500, which led to a frame shift causing premature transcription termination in arl1 mutant. Meanwhile, both deep sequencing and Sanger sequencing showed that Zm00001eb082520 was present in Gui18421 but was absent in arl1. A pair of near isogenic lines (NILs) carrying the Gui18421 allele (NIL^Gui18421) and the arl1 allele (NIL ^arl1 ) were developed, and the leaves of NIL ^arl1 plants had greater light transmission and photosynthetic rate in the middle and lower canopy than did those of NIL^Gui18421 plants under high-density planting. Furthermore, NIL ^arl1 had a higher seed setting rate, more kernels per ear, and an increased kernel weight per ear than NIL^Gui18421, and the grain yield of NIL ^arl1 was not affected as the planting density increased, suggesting that the arl1 locus can be used for genetic improvement of high-density planting tolerance. Taken together, the identification of arl1 and evaluation of yield-related traits for NIL^Gui18421 and NIL ^arl1 provide an excellent target for future maize improvement.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01534-0.

Tofu is a popular soybean (Glycine max (L.) Merr.) food with a long tradition in Asia and rising popularity worldwide, including Central Europe. Due to the labour-intensive phenotyping procedures, breeding for improved tofu quality is challenging. Therefore, our objective was to unravel the genetic architecture of traits relevant for tofu production in order to assess the potential of marker-assisted selection and genomic selection in breeding for these traits. To this end, we performed QTL mapping with 188 genotypes from a biparental mapping population. The population was evaluated in a two-location field trial, and tofu was produced in the laboratory to evaluate tofu quality. We identified QTL for all investigated agronomic and quality traits, each explaining between 6.40% and 27.55% of the genotypic variation, including the most important tofu quality traits, tofu yield and tofu hardness. Both traits showed a strong negative correlation (r = -0.65), and consequently a pleiotropic QTL on chromosome 10 was found with opposite effects on tofu hardness and tofu weight, highlighting the need to balance selection for both traits. Four QTL identified for tofu hardness jointly explained 68.7% of the genotypic variation and are possible targets for QTL stacking by marker-assisted selection. To exploit also small-effect QTL, genomic selection revealed moderate to high mean prediction accuracies for all traits, ranging from 0.47 to 0.78. In conclusion, inheritance of tofu quality traits is highly quantitative, and both marker-assisted selection and genomic selection present valuable tools to advance tofu quality by soybean breeding.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01529-x.

Black rice has a long history of cultivation in Asia especially China. As a whole grain, black rice is rich in diverse nutrients including proteins, vitamins, amino acids, minerals, unsaturated fatty acids, dietary fibers, alkaloids, carotenes, phenolic compounds, and anthocyanins, in addition to starch. Many studies have demonstrated a range of health-promoting effects by black rice, which has greatly attracted the attention of consumers. However, the production and consumption of black rice has been low mostly because of its poor cooking and eating quality. To address this problem, the first is a need for technology to evaluate the cooking and eating quality of black rice. In this study, we investigated the feasibility of using Rice Taste Evaluation System (RTES) as a proxy approach to eating and cooking quality evaluation of whole grain black rice (WGBR). Totally, 775 black rice samples obtained from 363 accessions harvested from field planting were evaluated both with sensory evaluation by panelists and with RTES consisting of a cooked rice taste analyzer and a hardness and stickiness meter, which produced 8 characteristic parameters. We obtained highly significant correlation (R ²  = 0.867, P < 2.2 × 10^-16) between sensory test scores and RTES values by multiple linear regression equation based on the selected variables, which was validated with just as high correlation, indicating that the RTES can provide equivalent results the sensory test. With the efficiency of this equipment, the RTES can provide a convenient and accurate tool for high throughput evaluation of cooking and eating quality of WGBR for breeding and other usages.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01535-z.

The phenotypes of chili pepper (Capsicum annuum) fruit are sometimes characterized by having either smooth or wrinkled surfaces, both of which are commercially important. However, as the inheritance patterns and responsible loci have not yet been identified, it is difficult to control fruit surface traits in conventional chili pepper breeding. To obtain new insights into these aspects, we attempted to clarify the genetic regulation mechanisms responsible for the wrinkled surface of fruit from the Japanese chili pepper 'Shishito' (C. annuum). First, we investigated the segregation patterns of fruit-surface wrinkling in F₂ progeny obtained from crosses between the C. annuum cultivars 'Shishito' and 'Takanotsume', the latter of which has a smooth fruit surface. The F₂ progeny exhibited a continuous variation in the level of wrinkling, indicating that the wrinkled surface in 'Shishito' was a quantitative trait. To identify the responsible loci, we performed quantitative trait locus (QTL) analysis of the F₂ progeny using restriction site-associated DNA sequencing data obtained in our previous study. The results showed that two significant QTLs (Wr11 and Wr12) were newly detected on chromosome 11 and 12, which explained 17.5 and 66.0% of the genetic variance, respectively. We then investigated the genetic effects of these QTLs using molecular markers. The findings showed that the levels of wrinkling in the F₂ progeny could mostly be explained by the independent additive effects of the 'Shishito' allele in Wr12. This locus was therefore considered to be a useful genomic region for controlling fruit surface traits in the chili pepper.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-024-01528-y.