Theoretical and Applied Genetics最新文献

Key message: Three computationally efficient algorithms of GP including RHBK, RHDK, and RHPK were developed in approximate genome-based kernel model. The drastically growing amount of genomic information contributes to increasing computational burden of genomic prediction (GP). In this study, we developed three computationally efficient algorithms of GP including RHBK, RHDK, and RHPK in approximate genome-based kernel model, which reduces dimension of genomic data via Nyström approximation and decreases the computational cost significantly thereby. According to the simulation study and real datasets, our three methods demonstrated predictive accuracy similar to or better than RHAPY, GBLUP, and rrBLUP in most cases. They also demonstrated a substantial reduction in computational time compared to GBLUP and rrBLUP in simulation. Due to their advanced computing efficiency, our three methods can be used in a wide range of application scenarios in the future.

Key message: Mutations in the CsEMS1 gene result in male sterility and reduced wart number and density. Male sterility and fruit wart formation are two significant agronomic characteristics in cucumber (Cucumis sativus), yet knowledge of our underlying genetics is limited. In this study, we identified an EMS-induced male sterility and few small warts mutant (msfsw). Histological observations revealed defects the absence of tapetum, meiotic aberration and impaired microspore formation in the anthers of the mutant. The mutant also exhibits a reduction in both the size and number of fruit spines and fruit tubercules. Genetic analysis revealed that a single recessive gene is responsible for the mutant phenotypes. BSA-Seq and fine genetic mapping mapped the msfsw locus to a 63.7 kb region with four predicted genes. Multiple lines of evidence support CsEMS1(CsaV3_3G016940) as the candidate for the mutant allele which encodes an LRR receptor-like kinase, and a non-synonymous SNP inside the exon of CsEMS1 is the causal polymorphisms for the mutant phenotypes. This function of CsEMS1 in determination of pollen fertility was confirmed with generation and characterization of multiple knockout mutations with CRISPR/Cas9 based gene editing. In the wild-type (WT) plants, CsEMS1 was highly expressed in male flowers. In the mutant, the expression level of CsEMS1, several tapetum identity-related genes, and trichome-related genes were all significantly reduced as compared with the wild-type. Protein-protein interaction assays revealed physical interactions between CsEMS1 and CsTPD1. Quantitation of endogenous phytohormones revealed a reduction in the ethylene precursor ACC in CsEMS1 knockout lines. This work identified an important role of CsEMS1 in anther and pollen development as well as fruit spine/wart development in cucumber.

Key message: Restoration of haploid female and haploid male fertility without colchicine is feasible. Three SNPs and eight gene models for HFF, and one SNP and a gene model for HMF were identified. Doubled haploid (DH) breeding accelerates the development of elite inbred lines and facilitates the incorporation of exotic germplasm, offering a powerful tool for maize improvement. Traditional DH breeding relies on colchicine to induce haploid genome doubling. Colchicine is toxic, and its application is labor-intensive, with most genotypes recording low genome doubling rates (10-30%). This study investigates spontaneous haploid genome doubling (SHGD) as a safer and more efficient alternative to colchicine. We evaluated the effectiveness of SHGD in restoring haploid female fertility (HFF) and haploid male fertility (HMF) without colchicine. Using genome-wide association studies (GWAS), we identified genomic regions influencing HFF and HMF. The plant materials included the BS39-haploid isogenic lines (HILs) and BS39-SHGD-haploid isogenic lines (HILs). Our results revealed significant SNP associations for both traits, with candidate genes involved in cell cycle regulation, cytoskeletal organization, and hormonal signaling. Analysis of variance (ANOVA) revealed significant variation in HFF across haploids and two environments. Similarly, HMF showed substantial differences across haploids and between the two environments. Spearman correlation between HFF and HMF showed no correlation (r = -0.03) between the two traits. HFF showed high heritability (0.8), indicating strong genetic control, whereas HMF displayed moderate heritability (0.5), suggesting additional environmental influences. The findings underscore the potential of SHGD to enhance DH breeding efficiency and support the development of new maize varieties tailored to diverse agricultural needs.

Key message: Map-based cloning revealed BhAPRR2, encoding a two-component response-regulating protein that regulates the black peel formation of mature fruit in wax gourd. Wax gourd is an economically significant vegetable crop, and peel color is a crucial agronomic trait that influences its commercial value. Although genes controlling light green or white peel have been cloned in wax gourd, the genetic basis and molecular mechanism underlying black peel remain unclear. Here, we confirmed that the peel color of wax gourd is a qualitative trait governed by single gene, with black being dominant over green. Through bulked segregant analysis sequencing (BSA-seq) and map-based cloning, we identified Bh.pf3chr5g483 as the candidate gene. This gene encodes a two-component response-regulating protein and is homologous to APRR2, referred to as BhAPRR2. Compared to P170, the BhAPRR2 in YD1 exhibits multiple mutations in both its coding and promoter regions. Notably, the mutations in the coding region do not affect its nuclear localization or transcriptional activation activity. However, the mutations in the promoter region substantially increase its expression in the peel of YD1, potentially contributing to the black peel phenotype observed in this variety. Furthermore, we developed an insertion/deletion (InDel) marker based on a 93-base pair (bp) insertion/deletion mutation in the promoter region of BhAPRR2, which achieved up to 95.8% phenotypic accuracy in a natural population comprising 165 wax gourd germplasms. In summary, our findings suggest that mutations in the promoter region of BhAPRR2 may contribute to the development of black peel in wax gourd. This discovery provides new insights into the molecular and genetic mechanisms underlying peel color diversity and offers a valuable molecular marker for wax gourd breeding efforts.

Key message: A physical map of Aegilops geniculata chromosome 7M^g was constructed, and a novel purple coleoptile gene was localized at 7M^gS bin FL 0.60-0.65 by development of wheat-Ae. geniculata structural aberrations. The development of wheat-wild relative chromosomal structure aberrations not only provides novel germplasm resources for wheat improvement, but also aids in mapping desirable genes to specific chromosomal regions. Aegilops geniculata (2n = 4x = 28, U^gU^gM^gM^g), a wild relative of common wheat, possesses many favorable genes. In this study, Ae. geniculata chromosome 7M^g was identified as harboring a purple coleoptile gene by phenotypic evaluation of Chinese Spring (CS)-Ae. geniculata addition and substitution lines. To construct a physical map of chromosome 7M^g and localize the purple coleoptile gene, 59 molecular markers specific to 7M^g were developed, and 43 wheat-Ae. geniculata 7M^g chromosome structure aberrations were generated based on chromosome centromeric breakage-fusion and ph1b-induced homoeologous recombination. Segment sizes and breakpoint positions of each 7M^g structure aberration were further characterized using in situ hybridization and molecular marker analysis. Consequently, a physical map of chromosome 7M^g was constructed with 59 molecular markers, comprising six bins with 28 markers on 7M^gS and six bins with 31 markers on 7M^gL, and the purple coleoptile gene was mapped to an interval of FL 0.60-0.65 on 7M^gS. The newly developed wheat-Ae. geniculata 7M^g structural aberrations and the physical map of 7M^g will facilitate the transfer and utilization of desirable genes from 7M^g in the future.

Key message: Transcriptomics- and FAME-GC-MS-assisted apomixis breeding generated Paspalum notatum hybrids with clonal reproduction and increased α-linolenic acid content, offering the potential to enhance livestock product's nutritional quality and reduce methane emissions A low omega-6:omega-3 fatty acid ratio is considered an indicator of the nutritional impact of milk fat on human health. In ruminants, major long-chain fatty acids, such as linoleic acid (18:2, omega-6) and α-linolenic acid (18:3, omega-3), originate from dietary sources and reach the milk via the bloodstream. Since forages are the primary source of long-chain fatty acids for such animals, they are potential targets for improving milk lipid composition. Moreover, a high 18:3 content in their diet is associated with reduced methane emissions during grazing. This work aimed to develop genotypes of the forage grass Paspalum notatum with high leaf 18:3 content and the ability for clonal reproduction via seeds (apomixis). We assembled diploid and polyploid Paspalum notatum leaf transcriptomes and recovered sequences of two metabolism genes associated with the establishment of lipid profiles, namely SUGAR-DEPENDENT 1 (SDP1) and PEROXISOMAL ABC TRANSPORTER 1 (PXA1). Primers were designed to amplify all expressed paralogs in leaves. qPCR was used to analyse SDP1 and PXA1 expression in seven divergent genotypes. Reduced levels of SDP1 and PXA1 were found in the polyploid sexual genotype Q4188. Fatty acid methyl esters/gas chromatography/mass spectrometry (FAME/GC/MS) assays confirmed an increased percentage of 18:3 in this genotype. Crosses between Q4188 and the obligate apomictic pollen donor Q4117 resulted in two apomictic F₁ hybrids (JS9 and JS71) with reduced SDP1 and PXA1 levels, increased 18:3 content, and clonal maternal reproduction. These materials could enhance milk and meat quality while reducing greenhouse gas emissions during grazing.

Key message: DDP1, encoding a β-Ketoacyl-CoA Synthase, regulates rice anther dehiscence and pollen fertility by affecting the deposition of lipid on anther epidermis and pollen wall. Anther dehiscence and pollen fertility are crucial for male fertility in rice. Here, we studied the function of Defective in Dehiscence and Pollen1 (DDP1), a novel member of the KCS family in rice, in regulating anther dehiscence and pollen fertility. DDP1 encodes an endoplasmic reticulum (ER)-localized protein and is ubiquitously expressed in various organs, predominately in the microspores and tapetum. The ddp1 mutant exhibited partial male sterility attributed to defective anther dehiscence and pollen fertility, which was notably distinct from those observed in Arabidopsis thaliana and rice mutants associated with lipid metabolism. Mutations of DDP1 altered the content and composition of wax on anther epidermis and pollen wall, causing abnormalities in their morphology. Moreover, genes implicated in lipid metabolism, pollen development, and anther dehiscence exhibited significantly altered expression levels in the ddp1 mutant. These findings indicate that DDP1 controls anther dehiscence and pollen fertility to ensure normal male development by modulating lipid homeostasis in the tapetum, thereby enhancing our understanding of the mechanisms underlying rice anther dehiscence and pollen fertility.

Key message: We derive formulas for the residual donor genome content during trait introgression via recurrent backcrossing and use these formulas to predict (without simulation) residual donor genome content for five future generations. Trait introgression is a common method for introducing valuable genes or alleles into breeding populations and inbred cultivars. The particular breeding scheme is usually designed to maximize the genetic similarity of the converted lines to the recurrent parent while minimizing cost and time to recover the near isogenic lines. Key variables include the number of generations and crosses and how to apply genotyping and selection. One form of trait introgression, which is our focus, involves an initial cross of an elite, homozygous recurrent parent line with a non-recurrent, homozygous donor line. The descendants of this cross are backcrossed with the recurrent parent for several generation before self-pollination in the final generation to recover lines with the alleles of interest. In this paper, we derive analytical formulas that characterize the stochastic nature of residual donor genome content during this form of trait introgression. The development of these formulas expands the mathematical methods one can integrate into breeding design. In particular, we show we can use our formulas in a novel mathematical program to allocate resources to optimize the reduction of residual donor genome content.

Key message: QTL-seq, linkage mapping, and whole-genome resequencing revealed a new locus (qCLS5.1) controlling Cercospora canescens resistance in mungbean and Receptor-like protein 12 (RLP12) genes as candidate genes for the resistance. Cercospora leaf spot (CLS) disease, caused by Cercospora canescens, is a common disease of mungbean (Vigna radiata). In this study, the genetics of CLS resistance was investigated in a new source of resistance (accession V2817) and the resistance was finely mapped to identify candidate genes. F₂ and F_2:3 populations of the cross V1197 (susceptible) × V2718 and a BC₁F₁ population of the cross V1197 × (V1197 × V2817) were used in this study. Segregation analysis suggested that the resistance is controlled by a single dominant gene. QTL-seq using F₂ individuals revealed that a single QTL (designated qCLS5.1) on chromosome 5 controlled the resistance. The qCLS5.1 was confirmed in the F_2:3 and BC₁F₁ populations by QTL analysis. Fine mapping using 978 F₂ individuals localized qCLS5.1 to a 48.94 Kb region containing three tandemly duplicated Receptor-like protein 12 (RLP12) genes. Whole-genome resequencing and alignment of V1197 and V2817 revealed polymorphisms causing amino acid changes and premature stop codons in the three RLP12 genes. Collectively, these results show that qCLS5.1 is a new locus for CLS resistance in mungbean, and a cluster of RLP12 genes are candidate genes for the resistance. The new locus qCLS5.1 will be useful for molecular breeding of durable CLS-resistant mungbean cultivars.

Key message: A powdery mildew (Pm) resistance locus PmRc1 was identified and transferred from Roegneria ciliaris into wheat. Two compensative translocation lines carrying PmRc1 were developed. Powdery mildew (Pm), caused by the biotrophic fungal pathogen Blumeria graminis f.sp. tritici (Bgt), is a global destructive disease of bread wheat (Triticum aestivum L.). Identifying and utilizing new Pm resistance gene(s) is the most fundamental work for disease control. Roegneria ciliaris (2n = 4 x= 28, genome S^cS^cY^cY^c) is a wild relative species of cultivated wheat. In this work, we evaluated wheat-R. ciliaris disomic chromosome addition lines for Pm resistance in multiple years. The introduction of R. ciliaris chromosome 1S^c into wheat enhanced resistance. The resistance locus on 1S^c was designated as PmRc1. To cytologically map PmRc1, we induced structural rearrangements using ion irradiation and increasing homoeologous chromosomal recombination. The identified 43 1S^c translocation or deletion lines were used to construct 1S^c cytological bin map by marker analysis using 111 molecular markers. Based on the Pm resistance of the characterized structural rearrangement lines, the PmRc1 locus was cytologically mapped to bin 1S^cS-8 of 1S^c short arm, flanked by markers CMH93-2 and CMH114-1. Two compensatory chromosomal translocation lines (T1S^cS $·$ 1BL and T1S^cS-1AS $·$ 1AL) carrying PmRc1 were developed and assessed for their agronomic traits. Translocation chromosome T1S^cS $·$ 1BL had enhanced Pm resistance accompanied by negative effects on grain number and single plant yield. Translocation chromosome T1S^cS-1AS $·$ 1AL had enhanced Pm resistance and increased spikelet number per spike, without any obvious negative effect on other tested traits. Thus, T1S^cS-1AS $·$ 1AL is recommended preferentially used in wheat breeding for Pm resistance.