Theoretical and Applied Genetics最新文献

Key message: A wild-allele GsPP2C-51-a1 of Glyma.14g162100 was identified in SojaCSSLP5, back to wild soybean, conferring drought tolerance. Its functions were verified in transgenic hairy root soybeans and Arabidopsis under water deficit and ABA treatment. A population of wild soybean chromosome segment substitution lines (CSSLs), SojaCSSLP5, with NN1138-2 as the cultivated recurrent parent and N24852 as the wild donor parent, was used to identify drought-tolerant loci/segments from the donor. Relative shoot dry weight, a tolerance indicator, varied significantly among the parents and CSSLs. Six drought tolerance loci/segments were detected in SojaCSSLP5, including Gm14_LDB_21 with GsPP2C-51 (Glyma.14g162100) as one of the four possible genes. This gene belongs to the F1 clade of protein phosphatase 2C based on gene ontology annotation, qPCR, and previous research results. Glyma.14g162100 was traced back to the Chinese germplasm population, in which four alleles existed on the locus, with soja holding all four, and max holding only two without any new alleles emerging. N24852 and NN1138-2 hold a1 and a2, respectively. The GsPP2C-51 protein was located inside the nucleus. In transgenic hairy root composite soybean, the GsPP2C-51-a1 overexpressed plants maintained a higher leaf fresh weight (tolerance) under 15% PEG stress compared to the empty vector plants. This was strongly supported by improved tolerance, chlorophyll content, and a series of physiological responses in GsPP2C-51-a1 overexpressed Arabidopsis plants under water deficit and abscisic acid treatments. Thus, the wild-type allele GsPP2C-51-a1 (Glyma.14g162100a1) from N24852 positively regulates plant drought tolerance.

Key message: Identified and validated QTL GpaVa_MRQ and GpaIX_MRQ provide robust tools for improving potato resistance to Globodera pallida via marker-assisted selection. Potato (Solanum tuberosum L.), a vital food crop globally, faces significant yield losses due to potato cyst nematodes (PCN). This study aimed to identify and validate genomic regions conferring resistance to Globodera pallida, to facilitate the development of resistant potato varieties through marker-assisted selection (MAS). We conducted Genome-Wide Association Studies (GWAS) on a pre-breeding panel genotyped using Genotyping by Sequencing (GBS) and the SolCAP DNA array. Significant resistance-associated SNP markers were identified on chromosomes III, IV, V, IX and XI. Quantitative trait loci (QTL), including the major-effect QTL GpaVa_MRQ on chromosome V and the QTL GpaIX_MRQ on chromosome IX, were validated and shown to account for substantial phenotypic variance in a validation potato panel. Haplotype-based marker sets were defined at four QTL regions, enabling the practical application of MAS. The successful conversion of SNPs to PACE markers at the two main QTL GpaVa_MRQ and GpaIX_MRQ further supports their use in breeding programs. This study provides valuable insights and robust tools for enhancing potato resistance to G. pallida, contributing to sustainable agricultural practices and global food security.

Leaf shape determines canopy structure and cotton productivity. Except for the L-D₁ locus, which determine the okra-leaf shape, the genetic control of other leaf shapes remains unknown in cotton. In the current study, using BSA-seq, RNA-seq, and molecular methods, GhRl₄ was mapped to chromosome A01, and it was identified as a key regulator of round-leaf shape in the cotton accession (M113116). Transcriptional suppression of GhRl₄ by virus-induced gene silencing (VIGS) led to the formation of leaf lobes and enlarged leaf size. Compared to the wild-type, the coding sequence of round-leaf alleles of GhRl₄ had a 21 bp deletion at the potential target site of miR319c. GhRl₄ belongs to the TCP (TEOSINTE BRANCHED1, CYCLODEA, and PROLIFERATING CELL FACTOR) 4 subfamily, previously implicated in the regulation of leaf shape in model plants. Further, transcriptome analysis indicated that PILS (PIN-LIKES), GIF (GRF-INTERACTING FACTOR), WIP (WIP DOMAIN PROTEIN), CUC (CUP-SHAPED COTYLEDON), and TCP family genes might be involved in the development of the round-leaf. Identifying the genetic and biochemical basis of phenotypic variation for leaf shape diversity would enable the use of genetic diversity and genomic tools for development of climate resilient high yielding cotton cultivars.

The Middle American rust resistance gene Ur-11 present in common bean (Phaseolus vulgaris L.) confers resistance to all but one known race of the pathogen Uromyces appendiculatus (Pers.) Unger. Even though progress has been made in understanding the host-pathogen interactions between common bean and U. appendiculatus, the causal alleles of the majority of rust resistance loci, including Ur-11, remain unknown. A genome-wide association study (GWAS) was conducted to identify genomic regions associated with resistance to the U. appendiculatus race 31-22, which is avirulent to Ur-11 but virulent to other Middle American rust resistance genes. GWAS using genotypic data consisting of approximately 70,959 SNP markers and phenotypic data based on the median reaction type (1-9 scale) of a panel of 357 Middle American breeding lines and cultivars, plus 5 germplasm lines with the Ur-11 locus derived from PI 181996, located Ur-11 on chromosome Pv11. Twenty-seven SNP markers clustered in the 55.16-55.56 Mb region of the P. vulgaris UI111 reference. Multiple DNA sequence alignments detected a missense mutation [c.1,328A > G] in the PvUI111.11G202400 gene model that encodes a leucine-rich repeat-containing protein in response to race 31-22. A PCR allele competitive extension marker (PACE) was developed and tested across a panel of ~ 700 Middle American dry bean genotypes. No recombination event was observed for the PACE marker among the tested genotypes; suggesting that the polymorphism on which it is based is very close to or in the Ur-11 gene. This PACE marker will be a useful and reliable marker for marker-assisted selection of Ur-11-based resistance to bean rust.

Seed germination is an essential stage in the life cycle of flowering plants, influencing the field emergence rates of seeds. Consequently, the role of GmAOC4 in soybean seed germination was investigated in the present study. Results suggested that the chloroplast-localized GmAOC4 exhibited high expression levels in the roots and young pods and during the seed germination stage in soybeans. It was found that GmAOC4 has been artificially selected during soybean domestication and improvement and that GmAOC4^H8 showed repressed seed germination, of which the frequency in landraces and cultivars decreased when compared with wild soybean. Knocking out GmAOC4^H8 via CRISPR/Cas9 led to enhanced germination in gmaoc4 mutants, suggesting its negative regulation on seed germination in soybeans. Additionally, decreased endogenous jasmonic acid (JA) and JA precursor, 12-oxo-phytodienoic acid, were found in gmaoc4 mutants. RNA-seq analyses revealed that 91 and 269 differentially expressed genes (DEGs) were up-regulated and down-regulated in gmaoc4 mutants, respectively. Among these DEGs, three genes were involved in JA biosynthetic and signaling pathways. Our results offer new insights into the mechanism of soybean seed germination regulation by GmAOC4.

Key message: A total of 4006 tropical and subtropical rice germplasms were screened for brown planthopper resistance, and the resistance mechanisms of 63 highly resistant accessions were characterized. This led to the designation of three novel resistance QTLs: Bph47, Bph48, and Bph49. The brown planthopper (BPH) is a significant piercing-sucking pest of rice plants that causes widespread destruction globally. Discovering new germplasms and genes for BPH resistance is essential for enhancing genetic diversity in rice breeding. In this study, 4006 rice accessions from tropical and subtropical regions were screened for BPH resistance at the seedling stage, and 63 accessions with high-resistant were identified. Of these, 59 accessions exhibited high resistance to BPH at the adult stage. The 63 accessions displayed widespread variation in key agronomic traits, though most were generally unsatisfactory. Assessments of antixenosis, antibiosis, and tolerance indicated diverse resistance mechanisms in the 63 accessions, with the majority (39/63) demonstrating both antixenosis and antibiosis. Microscopic observations and physiological assessments revealed significant differences in vascular bundle structure, fiber content, and activity of defense-related enzymes between the 63 high-resistance and 27 susceptible ones. Furthermore, correlation analysis highlighted a substantial positive relationship between BPH resistance and parameters such as rice trypsin inhibitor (RTI) levels and width of the sclerenchyma layer (WSL). Genetic analysis of F_2:3 segregating populations from four resistant accessions crossed with the susceptible rice variety 9311 identified three novel major-effect quantitative-trait loci (QTLs) located on chromosome 1L (690 kb and 1.84 Mb) and 5S (295 kb). This study significantly enriched the BPH-resistant germplasm sources and genes, highlighting the varied resistance mechanisms of rice against BPH.

Key message: The origin of common bean was investigated throughout chloroplast and nuclear WGS data considering recombination events. Our results support the Mesoamerican origin of common bean. The remarkable evolutionary history of the common bean (Phaseolus vulgaris L.) has led to the emergence of three wild main gene pools corresponding to three different eco-geographical areas: Mesoamerica, the Andes and northern Peru/Ecuador. Recent works proposed novel scenarios, and the northern Peru/Ecuador population has been described as a new species called P. debouckii, rekindling the debate about the origin of P. vulgaris. Here we shed light on the origin of P. vulgaris by analyzing the chloroplast and nuclear genomes of a large varietal collection representing the entire geographical distribution of wild forms including a large collection of Mesoamerican and Andean individuals. We assembled 37 chloroplast genomes de novo and used them to construct a time frame for the divergence of the genotypes under investigation, revealing that the separation of the Mesoamerican and northern Peru/Ecuador gene pools occurred ~ 0.15 Mya. Our results clearly support a Mesoamerican origin of the common bean and reject the recent P. deboukii hypothesis. These results also imply two independent migratory events from Mesoamerica to the North and South Andes, probably facilitated by birds. Our work represents a paradigmatic example of the importance of taking into account the genetic rearrangements produced by recombination when investigating phylogeny and of the analysis of wild forms when studying the evolutionary history of a crop species.

Key message: Spermidine production in the endophytic fungus Phomopsis liquidambaris is regulated by Sas3, and spermidine promotes resistance to Fusarium graminearum by increasing the expression of immune-related indicators in wheat. Fusarium head blight (FHB) is a common wheat disease caused mainly by Fusarium graminearum. The present study showed that overexpression of the histone acetyltransferase Sas3 in Phomopsis liquidambaris regulated the synthesis of spermidine and promoted resistance to F. graminearum in wheat. Sas3 localized in the nucleus plays a key role in acetylating lysines 9 and 14 of histone H3 (H3K9 and H3K14) and clearly promotes the development and growth of P. liquidambaris in the overexpression strain OE-Sas3 and knockout strain Ko-Sas3. The OE-Sas3 strain promoted the growth of wheat seedlings and increased the level of reactive oxygen species (ROS) pumps, which increased the activities of the catalase (CAT) and peroxidase (POD) and the expression levels of genes involved in the jasmonic acid, ethylene, and salicylic acid pathways. Furthermore, OE-Sas3 increased the level of resistance of wheat to F. graminearum through the positive regulation of spermidine biosynthesis, which reduced the incidence of wheat spike disease from 76 to 54% and that of grain disease from 52.35 to 32.68%. This study provides a new perspective for the application of P. liquidambaris as a biocontrol agent via rational design and improved FHB resistance.

Key message: Submergence tolerance QTLs for rice germination were identified via a genome-wide association study, and a new causal gene, LOC_Os06g17260, was identified. Submergence stress is a major obstacle limiting the application of direct seeding in rice cultivation. Rapid bud and root growth helps plants establish a stronger growth base and improve their submergence tolerance. Therefore, mining genes for bud length (BL) and root length (RL) helps in the development of varieties that are adaptable to submergence and improve seedling emergence and yield of direct-seeded rice. In this study, a genome-wide association study of BL and RL was performed on a diverse rice collection consisting of 300 accessions. We identified a total of 37 QTLs, 13 of which had phenotypic contributions > 10%. The novel QTLs qBL6.2/qRL6.8, qBL6.3/qRL6.9, qBL6.4/qRL6.10, and qBL6.5/qRL6.11 on chromosome 6 were stably detected across BL and RL, and a total of 31 genes were detected in these four intervals. Concerning the gene annotation information and expression profiles, LOC_Os06g17090, LOC_Os06g17120, LOC_Os06g17140, LOC_Os06g17220, and LOC_Os06g17260 were selected as possible target genes. Through the validation of a knockout transgenic experiment, LOC_Os06g17260 was identified as the causal gene for submergence tolerance in rice at the germination stage. LOC_Os06g17260 encodes UDP-glucoronosyl and a UDP-glucosyl transferase domain-containing protein and contains two major haplotypes, with the Hap1 germplasm presenting greater submergence tolerance at the germination stage. These results provide new clues for exploring the molecular mechanisms that regulate submergence tolerance in rice and provide a promising source of genes for the molecular breeding of direct-seeded rice.

Key message: A novel major QTL, QTkw.cau-3DL, for thousand-kernel weight has been identified on the wheat chromosome arm 3DL and enhances grain yield by 6.2% under field conditions. Increasing kernel weight is an effective way to improve yield potential in wheat. The identification of major quantitative trait loci (QTL) for kernel weight, without negative effects on other yield-related traits, is crucial for continuous yield improvement. We developed a population of F₆ recombinant inbred lines from Jimai 120 × Jimai 325 and identified eight QTL for thousand-kernel weight, kernel length, and kernel width across five environments. The population was genotyped using Wheat15K SNP arrays and QTL analysis found that one QTL, QTkw.cau-3DL, on the chromosome arm 3DL consistently showed major effects on TKW and KL in five field experiments. This QTL accounted for up to 16.43% and 13.87% of phenotypic variation, respectively. QTkw.cau-3DL was confined to a 5.72-Mb (3.48 cM) interval between 554.39 Mb and 560.11 Mb. This QTL was validated in a pair of NILs and in a new population. QTkw.cau-3DL increased kernel weight per spike without any negative effect on heading data, plant height, spike length, spikelet number per spike, or kernels number per spike. It increased grain yield by 6.2% under regular field production conditions. Haplotype analysis and geographical distribution in a nationwide collection of 630 wheat cultivars showed that QTkw.cau-3DL has not been widely deployed in Chinese wheat breeding programs. QTkw.cau-3DL is a novel QTL for increasing TKW through increasing KL; therefore, it is an important locus for enhancing wheat grain yield. The tightly linked, user-friendly markers developed in this study should facilitate map-based cloning and marker-assisted selection of the QTL in wheat breeding programs.