Theoretical and Applied Genetics最新文献

Key message: Two major QTLs for cold tolerance in pumpkin were localised, and CmoERF017 was identified as a key candidate gene within these QTLs via RNA-seq. Functional analysis revealed that CmoERF017 was a positive regulator of pumpkin in response to low-temperature stress. Low temperature is a key environmental factor that affects the protected cultivation of cucumber (Cucumis sativus L.) in winter, and the cold tolerance of cucumber/pumpkin-grafted seedlings depends on the rootstock. Pumpkin (Cucurbita spp.) has a well-developed root system, high resistance and wide adaptation, commonly used as rootstock for cucumber to improve the cold tolerance of grafted seedlings. This study used two high-generation inbred lines of Cucurbita moschata with significant differences in cold tolerance. We identified key candidate genes within the major cold tolerance QTL of rootstocks using QTL-seq and RNA-seq and investigated the function and molecular mechanisms of these genes in response to low-temperature stress. Results showed that QTL-seq located two cold tolerance QTLs, qCII-1 and qCII-2, while RNA-seq located 28 differentially expressed genes within these QTLs. CmoERF017 was finally identified as a key candidate gene. Functional validation results indicated that CmoERF017 is a positive regulator of pumpkin in response to low-temperature stress and affected root ABA synthesis and signalling by directly regulating the expression of SDR7 and ABI5. This study identified a key gene for low-temperature stress tolerance in rootstock pumpkin and clarified its role in the molecular mechanism of hormone-mediated plant cold tolerance. The study findings enrich the theoretical understanding of low-temperature stress tolerance in pumpkin and are valuable for the selection and breeding of cold-tolerant varieties of pumpkin used for rootstocks.

Key message: A major and stable QTL for sterile florets per spike and sterile florets per spikelet was identified, it was mapped within a 2.22-Mb interval on chromosome 5AL, and the locus was validated using two segregating populations with different genetic backgrounds. Both the number of fertile florets per spike (FFS) and the number of sterile florets per spike (SFS) significantly influence the final yield of wheat (Triticum aestivum L.), and a trade-off theoretically exists between them. To enhance crop yield, wheat breeders have historically concentrated on easily measurable traits such as FFS, spikelets per spike, and spike length. Other traits of agronomic importance, including SFS and sterile florets per spikelet (SFPs), have been largely overlooked. In the study, reported here, genetic bases of SFS and SFPs were investigated based on the assessment of a population of recombinant inbred lines (RILs) population. The RIL population was developed by crossing a spontaneous mutant with higher SFS (msf) with the cultivar Chuannong 16. A total of 10 quantitative trait loci (QTL) were identified, with QSFS.sau-MC-5A for SFS and QSFPs.sau-MC-5A for SFPs being the major and stable ones, and they were co-located on the long arm of chromosome 5A. The locus was located within a 2.22-Mb interval, and it was further validated in two additional populations based on a tightly linked Kompetitive Allele-Specific PCR (KASP) marker, K_sau_5A_691403852. Expression differences and promoter sequence variations were observed between the parents for both TraesCS5A03G1247300 and TraesCS5A03G1250300. The locus of QSFS.sau-MC-5A/QSFPs.sau-MC-5A showed a significantly positive correlation with spike length, florets in the middle spikelet, and total florets per spike, but it showed no correlation with either kernel number per spike (KNS) or kernel weight per spike. Appropriate nitrogen fertilizer application led to reduced SFS and increased KNS, supporting results from previous reports on the positive effect of nitrogen fertilizer on wheat spike and floret development. Based on these results, we propose a promising approach for breeding wheat cultivars with multiple fertile florets per spike, which could increase the number of kernels per spike and potentially improve yield. Collectively, these findings will facilitate further fine mapping of QSFS.sau-MC-5A/QSFPs.sau-MC-5A and be instrumental in strategies to increase KNS, thereby enhancing wheat yield.

Key message: qPEDS1, a major quantitative trait locus that determines kernel row number during domestication, harbors the proposed causal gene Zm00001d033675, which may affect jasmonic acid biosynthesis and determine the fate of spikelets. Maize domestication has achieved the production of maize with enlarged ears, enhancing grain productivity dramatically. Kernel row number (KRN), an important yield-related trait, has increased from two rows in teosinte to at least eight rows in modern maize. However, the genetic mechanisms underlying this process remain unclear. To understand KRN domestication, we developed a teosinte-maize BC₂F₇ population by introgressing teosinte into a maize background. We identified one line, Teosinte ear rank1 (Ter1), with only 5-7 kernel rows which is fewer than those in almost all maize inbred lines. We detected two quantitative trait loci underlying Ter1 and fine-mapped the major one to a 300-kb physical interval. Two candidate genes, Zm674 and Zm675, were identified from 26 maize reference genomes and teosinte bacterial artificial chromosome sequences. Finally, we proposed that Ter1 affects jasmonic acid biosynthesis in the developing ear to determine KRN by the fate of spikelets. This study provides novel insights into the genetic and molecular mechanisms underlying KRN domestication and candidates for de novo wild teosinte domestication.

Key message: A major QTL, qLF2.1, for flowering time in tomatoes, was fine mapped to chromosome 2 within a 51.37-kb interval, and the SlJMJ14 gene was verified as the causal gene by knockout. Tomato flowering time is an important agronomic trait that affects yield, fruit quality, and environmental adaptation. In this study, the high-generation inbred line 19108 with a late-flowering phenotype was selected for the mapping of the gene that causes late flowering. In the F₂ population derived from 19108 (late flowering) × MM (early flowering), we identified a major late-flowering time quantitative trait locus (QTL) using QTL-seq, designated qLF2.1. This QTL was fine mapped to a 51.37-kb genomic interval using recombinant analysis. Through functional analysis of homologous genes, Solyc02g082400 (SlJMJ14), encoding a histone demethylase, was determined to be the most promising candidate gene. Knocking out SlJMJ14 in MM resulted in a flowering time approximately 5-6 days later than that in the wild-type plants. These results suggest that mutational SlJMJ14 is the major QTL for the late-flowering phenotype of the 19108 parental line.

Key message

From simulations and experimental data, the quality of cross progeny variance genomic predictions may be high, but depends on trait architecture and necessitates sufficient number of progenies.

Abstract

Genomic predictions are used to select genitors and crosses in plant breeding. The usefulness criterion (UC) is a cross-selection criterion that necessitates the estimation of parental mean (PM) and progeny standard deviation (SD). This study evaluates the parameters that affect the predictive ability of UC and its two components using simulations. Predictive ability increased with heritability and progeny size and decreased with QTL number, most notably for SD. Comparing scenarios where marker effects were known or estimated using prediction models, SD was strongly impacted by the quality of marker effect estimates. We proposed a new algebraic formula for SD estimation that takes into account the uncertainty of the estimation of marker effects. It improved predictions when the number of QTL was superior to 300, especially when heritability was low. We also compared estimated and observed UC using experimental data for heading date, plant height, grain protein content and yield. PM and UC estimates were significantly correlated for all traits (PM: 0.38, 0.63, 0.51 and 0.91; UC: 0.45, 0.52, 0.54 and 0.74; for yield, grain protein content, plant height and heading date, respectively), while SD was correlated only for heading date and plant height (0.64 and 0.49, respectively). According to simulations, SD estimations in the field would necessitate large progenies. This pioneering study experimentally validates genomic prediction of UC but the predictive ability depends on trait architecture and precision of marker effect estimates. We advise the breeders to adjust progeny size to realize the SD potential of a cross.

Key message

We identified a 580 bp deletion of CmaKNAT6 coding region influences peel colour of mature Cucurbita maxima fruit.

Abstract

Peel colour is an important agronomic characteristic affecting commodity quality in Cucurbit plants. Genetic mapping of fruit peel colour promotes molecular breeding and provides an important basis for understanding the regulatory mechanism in Cucurbit plants. In the present study, the Cucurbita maxima inbred line ‘9-6’ which has a grey peel colour and ‘U3-3-44’ which has a dark green peel colour in the mature fruit stage, were used as plant materials. At 5–40 days after pollination (DAP), the contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoids in the ‘U3-3-44’ peels were significantly greater than those in the ‘9-6’ peels. In the epicarp of the ‘9-6’ mature fruit, the presence of nonpigmented cell layers and few chloroplasts in each cell in the pigmented layers were observed. Six generations derived by crossing ‘9-6’ and ‘U3-3-44’ were constructed, and the dark green peel was found to be controlled by a single dominant locus, which was named CmaMg (mature green peel). Through bulked-segregant analysis sequencing (BSA-seq) and insertion-deletion (InDel) markers, CmaMg was mapped to a region of approximately 449.51 kb on chromosome 11 using 177 F₂ individuals. Additionally, 1703 F₂ plants were used for fine mapping to compress the candidate interval to a region of 32.34 kb. Five coding genes were in this region, and CmaCh11G000900 was identified as a promising candidate gene according to the reported function, sequence alignment, and expression analyses. CmaCh11G000900 (CmaKNAT6) encodes the homeobox protein knotted-1-like 6 and contains 4 conserved domains. CmaKNAT6 of ‘9-6’ had a 580 bp deletion, leading to premature transcriptional termination. The expression of CmaKNAT6 tended to increase sharply during the early fruit development stage but decrease gradually during the late period of fruit development. Allelic diversity analysis of pumpkin germplasm resources indicated that the 580 bp deletion in the of CmaKNAT6 coding region was associated with peel colour. Subcellular localization analysis indicated that CmaKNAT6 is a nuclear protein. Transcriptomic analysis of the inbred lines ‘9-6’ and ‘U3-3-44’ indicated that genes involved in chlorophyll biosynthesis were more enriched in ‘U3-3-44’ than in ‘9-6’. Additionally, the expression of transcription factor genes that positively regulate chlorophyll synthesis and light signal transduction pathways was upregulated in ‘U3-3-44’. These results lay a foundation for further studies on the genetic mechanism underlying peel colour and for optimizing peel colour-based breeding strategies for C. maxima.

Key message

Single nucleotide polymorphism (SNP) markers in wheat and their prospects in breeding with special reference to rust resistance.

Abstract

Single nucleotide polymorphism (SNP)-based markers are increasingly gaining momentum for screening and utilizing vital agronomic traits in wheat. To date, more than 260 million SNPs have been detected in modern cultivars and landraces of wheat. This rapid SNP discovery was made possible through the release of near-complete reference and pan-genome assemblies of wheat and its wild relatives, coupled with whole genome sequencing (WGS) of thousands of wheat accessions. Further, genotyping customized SNP sites were facilitated by a series of arrays (9 to 820Ks), a cost effective substitute WGS. Lately, germplasm-specific SNP arrays have been introduced to characterize novel traits and detect closely linked SNPs for marker-assisted breeding. Subsequently, the kompetitive allele-specific PCR (KASP) assay was introduced for rapid and large-scale screening of specific SNP markers. Moreover, with the advances and reduction in sequencing costs, ample opportunities arise for generating SNPs artificially through mutations and in combination with next-generation sequencing and comparative genomic analyses. In this review, we provide historical developments and prospects of SNP markers in wheat breeding with special reference to rust resistance where over 50 genetic loci have been characterized through SNP markers. Rust resistance is one of the most essential traits for wheat breeding as new strains of the Puccinia fungus, responsible for rust diseases, evolve frequently and globally.

Key message

Mutations in TaCHLI impact chlorophyll levels and yield-related traits in wheat.Natural variations in TaCHLI-7A/B influence plant productivity, offering potential for molecularbreeding.

Abstract

Chlorophyll is essential for plant growth and productivity. The CHLI subunit of the magnesium chelatase protein plays a key role inserting magnesium into protoporphyrin IX during chlorophyll biosynthesis. Here, we identify a novel wheat mutant chlorophyll (chl) that exhibits yellow-green leaves, reduced chlorophyll levels, and increased carotenoid content, leading to an overall decline in yield-related traits. Map-based cloning reveals that the chl phenotype is caused by a point mutation (Asp186Asn) in the TaCHLI-7D gene, which encodes subunit I of magnesium chelatase. Furthermore, the three TaCHLI mutants: chl-7b-1 (Pro82Ser), chl-7b-2 (Ala291Thr), and chl-7d-1 (Gly357Glu), also showed significant reductions in chlorophyll content and yield-related traits. However, TaCHLI-7D overexpression in rice significantly decreased thousand kernel weight, yield per plant, and germination. Additionally, natural variations in TaCHLI-7A/B are significantly associated with flag leaf, spike exsertion length, and yield per plant. Notably, the favorable haplotype, TaCHLI-7B-HapII, which displayed higher thousand kernel weight and yield per plant, is positively selected in wheat breeding. Our study provides insights on the regulatory molecular mechanisms underpinning leaf color and chlorophyll biosynthesis, and highlights TaCHLI functions, which provide useful molecular markers and genetic resources for wheat breeding.

Key messages

Sixty-nine quantitative trait nucleotides conferring maize resistance to Gibberella ear rot were detected, including eighteen novel loci. Four candidate genes were predicted, and four kompetitive allele-specific PCR markers were developed.

Abstract

Maize Gibberella ear rot (GER), caused by Fusarium graminearum, is one of the most devastating diseases in maize-growing regions worldwide. Enhancing maize cultivar resistance to this disease requires a comprehensive understanding of the genetic basis of resistance to GER. In this study, 334 maize inbred lines were phenotyped for GER resistance in five environments and genotyped using the Affymetrix CGMB56K SNP Array, and a genome-wide association study of resistance to GER was performed using a 3V multi-locus random-SNP-effect mixed linear model. A total of 69 quantitative trait nucleotides (QTNs) conferring resistance to GER were detected, and all of them explained individually less than 10% of the phenotypic variation, suggesting that resistance to GER is controlled by multiple minor-effect genetic loci. A total of 348 genes located around the 200-kb genomic region of these 69 QTNs were identified, and four of them (Zm00001d029648, Zm00001d031449, Zm00001d006397, and Zm00001d053145) were considered candidate genes conferring susceptibility to GER based on gene expression patterns. Moreover, four kompetitive allele-specific PCR markers were developed based on the non-synonymous variation of these four candidate genes and validated in two genetic populations. This study provides useful genetic resources for improving resistance to GER in maize.