Search Results (60)

The simultaneous improvement of fiber strength (FS) and lint percentage (LP) is a critical objective for achieving high-quality and high-yield cotton production. Identifying key genes and their regulatory networks that govern the synergistic development of FS and LP is essential for achieving their simultaneous improvement. In our previous study, a stable chromosome segment, Seg-D06-2, was identified for its ability to concurrently enhance both FS and LP with high reliability. In the present study, homozygous individuals harboring the Seg-D06-2 segment within a nearly uniform genetic background were selected to construct a large BC₆F₂ chromosome segment substitution line (CSSL) population comprising 3324 individuals. Extreme individuals characterized by simultaneous improvement in FS and LP, which shared similar genetic and phenotypic backgrounds, were subjected to comparative transcriptomic and weighted gene co-expression network analysis (WGCNA) at 0, 5, 10, 15, 20, and 25 days post-anthesis (DPA). The results highlighted the ’blue’ and ’yellow’ modules as being significantly associated with the simultaneous improvement of FS and LP. Four hub genes (GH_D06G0542, GH_D06G1609, GH_D06G0627 and GH_D06G2689) and two DEGs (GH_D06G0564 and GH_D06G0723) were identified in the ’blue’ module. Three hub genes (GH_D06G0540, GH_D06G0558 and GH_D06G0636) and one DEG (GH_D06G0527) were identified in the ’yellow’ module. These 10 key genes likely play pivotal roles in regulating the synergistic development of FS and LP, warranting further investigation. The reliability of the RNA-seq data was confirmed by qRT-PCR. This study provides a valuable resource for molecular breeding aimed at the simultaneous improvement of FS and LP and offers new insights into the molecular mechanisms governing their synergistic development. Full article

Background/Objectives: The significant negative correlation between protein and oil content in soybean seeds is a long-standing bottleneck for conventional breeding. Its root cause lies in insufficient understanding of related molecular regulatory processes. Methods: We selected the CSSL_R19, a chromosome segment substitution line, to thoroughly investigate the intrinsic effects of the substituted segment on the high seed storage protein (SSP) and low fatty acid (FA) phenotype. Transcriptomic, proteomic, and metabolomic analyses were performed on the recurrent parent and R19. Results: A total of 1821 differentially expressed genes (DEGs), 12 differentially expressed proteins (DEPs), and 10 differentially accumulated metabolites (DEMs) were detected. Subsequently, an integrative examination of the data demonstrated that 28 DEGs, 5 DEPs, and 4 DEMs participated in biological processes such as carbohydrate metabolism, lipid degradation, as well as protein synthesis and transport. Mechanistically, down-regulation of PGM reduces the carbon source supply for FA synthesis; up-regulation of LOX, LACS, ACX, and KAT promotes FA degradation. SRP, SAR1, and HSP70 are involved in the synthesis and transport of SSP. Crucially, qRT-PCR validation performed on all 28 core DEGs showed that their expression trends were highly consistent with the transcriptome data, confirming the reliability of the findings. Conclusions: In conclusion, we propose a potential regulatory network that enhances SSP accumulation and reduces FA content. Altogether, these findings advance our understanding of storage compound accumulation in soybeans and guide future breeding strategies. Full article

Rice yield is a complex quantitative trait. Although a lot of genes for yield have been cloned, their genetic basis remains unknown. In the present study, a set of chromosome segment substitution line population (CSSL) was developed, derived from the indica variety Huanghuazhan as the recipient parent and the Aus variety N22 as the donor parent, and a high-density bin map containing 609 bins was constructed by resequencing. The CSSL population comprised 155 families with an average background recovery rate of 93.02%. Nine yield-related traits, including plant height, panicle number, panicle length, primary branch number, spikelet number per panicle, grain number per panicle, seed setting rate, 1000-grain weight, and grain yield per plant, were evaluated across four environments. The results showed significant differences in yield-related traits between the two parents across four environments. All nine traits showed continuous distribution with transgressive segregation. Spikelet number per panicle, grain number per panicle and 1000-grain weight showed strong correlations with each other, whereas panicle number had weak correlations with them. A total of 80 main-effect quantitative trait loci (QTLs) affecting yield-related traits were identified, among which 13 QTLs were repeatedly detected in multiple environments, 45 QTLs were located in 8 pleiotropic QTL regions, and 47 QTLs showed significant interactions with environments. In addition, 260 pairs of epistatic QTLs underlying yield-related traits were identified, of which 2 pairs stably expressed across different environments, and 11 pairs controlled more than two traits. These findings provide a theoretical basis for clarifying the genetic differentiation between indica and Aus and cloning yield-related genes, and offer valuable gene resources for molecular breeding of high-yield rice varieties. Full article

Seed vitality is a key factor for successful germination of seeds and successful root establishment of crops. However, a cold environment can severely hinder the germination of soybean seeds, resulting in a significant decrease in yield. In this study, the cold tolerance of 205 chromosome segment substitution lines (CSSL) during the germination process was evaluated. CSSL_R22 exhibited higher seed vitality under low-temperature conditions. Five quantitative trait loci (QTL) related to cold tolerance during the germination stage were detected. By combining the QTL analysis results with transcriptome data, we determined that GmKAN1 (Glyma.20G108600) is an important regulatory factor for cold tolerance during seed germination. Preliminary studies have shown that GmKAN1, as a transcriptional repressor of GmARF2 and GmARF8, can regulate auxin synthesis to enhance the tolerance of seeds to cold stress. These results provide valuable insights into the regulatory network related to cold tolerance during soybean seed germination. Full article

Soybean (Glycine max L. Merr.) is rich in proteins, fats, and other nutrients, and the genetic improvement of soybean protein content has long been a key research focus in breeding programs. Based on the chromosome segment substitution line (CSSL) population, this study screened target lines within this population using genotypic and phenotypic information to establish an initial mapping population for soybean seed protein content. Through single-marker analysis, a quantitative trait locus (QTL) interval was mapped to the region between 26,705,080 bp and 33,180,908 bp on chromosome 16, designated as qSPJ_1. A secondary segregating population was constructed based on the initial mapping results for fine mapping, which narrowed the interval to 0.076 Mb. A total of 9 candidate genes were identified within this interval. By comparing amino acid and promoter sequences between the two parents, performing quantitative real-time PCR (qRT-PCR) analysis, and conducting haplotype analysis, Glyma.16G165100 was preliminarily predicted as a candidate gene affecting soybean seed protein content. The single nucleotide polymorphism (SNP) variation sites in its promoter region were significantly associated with the variation in protein content in the resource population. This study provides important theoretical guidance for dissecting the genetic mechanism of soybean seed protein content and advancing its breeding improvement. Full article

Kernel row number (KRN) is a pivotal determinant for yield in maize breeding programs. However, the genetic basis underlying KRN remains largely elusive. To identify candidate genes regulating KRN, a population of 318 BC₄F₄ chromosomal segment substitution lines (CSSLs) was developed via backcrossing, with Baimaya (BMY) as the donor parent and B73 as the recurrent parent. Furthermore, a high-density genetic linkage map containing 2859 high-quality single-nucleotide polymorphism (SNP) markers was constructed for quantitative trait locus (QTL) mapping of KRN. Notably, 19 QTLs controlling KRN were detected across three environments and in the Best Linear Unbiased Prediction (BLUP) values; among these, a major-effect QTL (qKRN4.09-1) was consistently identified across all three environments and BLUP. Then, the integration of linkage mapping and transcriptome analysis of 5 mm immature ears from near-isogenic lines (NILs) uncovered a candidate gene, Zm00001eb205550. This gene exhibited significant downregulation in qKRN4.09-1^BMY, and two missense variants were detected between qKRN4.09-1^BMY and qKRN4.09-1^B73. Zm00001eb205550 exhibited preferential expression in developing ears. Moreover, the pyramiding of favorable alleles from the five stable QTLs significantly increased KRN in maize. These findings advance our genetic understanding of maize ear development and provide valuable genetic targets for improving KRN in maize breeding. Full article

Soybean (Glycine max), as an important crop for both oil and grains, is a major source of high-quality plant proteins for humans. Among various natural disasters affecting soybean production, waterlogging is one of the key factors leading to yield reduction. It can cause root rot and seedling death, and in severe cases, even total crop failure. Given the significant differences in responses to waterlogging stress among different soybean varieties, traditional single-trait indicators are insufficient to comprehensively evaluate flood tolerance. In this study, relative seedling length (RSL) was used as a comprehensive evaluation index for flood tolerance. Using a chromosome segment substitution line (CSSL) population derived from SN14 and ZYD00006, we successfully identified seven quantitative trait loci (QTLs) associated with seed waterlogging tolerance. By integrating RNA-Seq transcriptome sequencing and phenotypic data, the functions of candidate genes were systematically verified. Phenotypic analysis indicated that Suinong14 had significantly better flood tolerance than ZYD00006. Further research revealed that the Glyma.05G160800 gene showed a significantly up-regulated expression pattern in Suinong14; qPCR analysis revealed that this gene exhibits higher expression levels in submergence-tolerant varieties. Haplotype analysis demonstrated a significant correlation between different haplotypes and phenotypic traits. The QTLs identified in this study can provide a theoretical basis for future molecular-assisted breeding of flood-tolerant varieties. Additionally, the functional study of Glyma.05G161800 in regulating seed flood tolerance can offer new insights into the molecular mechanism of seed flood tolerance. These findings could accelerate the development of submergence-tolerant rice varieties, enhancing crop productivity and stability in flood-prone regions. Full article

Salt stress severely constrains global crop productivity. However, most sweet corn cultivars exhibit weak tolerance to salt stress. In this study, two sweet corn CSSLs, salt-tolerant line D55 and salt-sensitive line D96, were selected as materials. We conducted comparative phenotyping and physiological profiling of seedlings under salinity treatment, and transcriptome analysis was carried out by sampling root tissues at 0 h, 4 h, 12 h, and 72 h post-treatment. The results indicated that D55 exhibited enhanced seedling height, root length, fresh weight, relative chlorophyll content, and antioxidant enzyme activities, while showing reduced malondialdehyde accumulation in comparison to D96. Pairwise comparisons across time points (0 h, 4 h, 12 h, 72 h) identified 6317 and 6828 differentially expressed genes (DEGs) in D55 and D96. A total of 49 shared DEGs across four time points were identified in D55 and D96, which were enriched in 12 significant Gene Ontology (GO) terms. Only eight DEGs were shared between genotypes across all comparisons. Transcriptomic analysis revealed 1281, 1946, and 1717 DEGs in genotypes D55 and D96 at 4 h, 12 h, and 72 h post-salt treatment, respectively. Genes associated with reactive oxygen species (ROS) homeostasis, phenylpropanoid metabolism, cutin, suberin and wax biosynthesis, and benzoxazinoid synthesis exhibit enhanced sensitivity in the salt-tolerant genotype D55. This leads to an enhanced ROS scavenging capacity and the establishment of a multi-layered defense mechanism. Additionally, brassinosteroid (BR), gibberellin (GA), and abscisic acid (ABA) and auxin-related genes exhibited different responses to salt stress in sweet corn. A hypothetical model, which established a multi-layered salt adaptation strategy, by integrating ROS detoxification, osmotic balance, and phytohormone signaling, was put forward. By integrating transcriptome and differential chromosomal fragment data, our findings identify 14 candidate genes for salt tolerance, providing potential ideal target genes in breeding to improve salt tolerance in sweet corn. Full article

Background: CCCH zinc finger proteins (OsC3Hs) are a class of transcriptional regulators that play important roles in plant development and stress responses. Although their functional significance has been widely studied in model species, comprehensive genome-wide characterization of CCCH proteins in rice (Oryza sativa) remains limited. Methods: Using Arabidopsis CCCH proteins as references, we identified the CCCH gene family in rice and analyzed the physicochemical properties, subcellular localization, conserved structures, phylogeny, cis-regulatory elements, synteny analysis, spatiotemporal expression patterns, and expression patterns under drought, ABA, and MeJA treatments for the identified CCCH family members. Results: The results showed that the rice CCCH family comprises 73 members, which are unevenly distributed across the 12 chromosomes. Phylogenetic analysis classified them into 11 subfamilies. Subcellular localization indicated that most members are localized in the nucleus. The upstream regions of CCCH promoters contain a large number of cis-regulatory elements related to plant hormones and biotic stress responses. Most genes respond to drought, abscisic acid (ABA), and methyl jasmonate (MeJA) treatments. OsC3H36 was highly expressed under drought, ABA, and MeJA treatments. Haplotype analysis of this gene revealed two major allelic variants (H1 and H2), with H1 predominantly found in japonica rice and associated with increased grain width and 1000-grain weight. Functional validation using a chromosome segment substitution line (CSSL1) confirmed these findings. Conclusions: CCCH genes play important roles in rice growth, development, and stress responses. Additionally, we validated that OsC3H36 is associated with rice grain width and 1000-grain weight. Full article

Awn length is a significant agronomic trait in rice. To analyze the genetic mechanism of awn length in the chromosome segment substitution line 29 (CSSL29) derived from 9311 (recipient) into Nipponbare (NIP, donor), an F₂ segregated population was constructed from 9311 (indica) and CSSL29. The population and candidate genes were analyzed using quantitative trait loci sequencing (QTL-seq), yeast two-hybrid assays, and 3 k and 10 k rice population databases. The results indicated that the awn length in the F₂ segregating population followed a normal distribution, and the long-awn phenotype in CSSL29 was controlled by multiple genes. Through BSA sequencing data, a major QTL qAWN4 associated with rice awn length was identified on chromosome 4, containing the cloned gene An-2. Further investigation of the CSSL29 long-awn substitution segment revealed the presence of the awn length gene An-1, with both genes exhibiting an additive effect on the regulation of the long-awn phenotype. Yeast two-hybrid experiments confirmed no interaction between An-2 and An-1, suggesting that additive effect awn length regulation is not mediated through simple protein-to-protein binding. Population genetic analysis indicated that the An-2 allele was artificially selected during domestication but did not significantly differ between indica and japonica subspecies. These findings enhance our understanding of the genetic regulation of rice awn length and the domestication of long-awn rice, laying the groundwork for future research in this area. Full article

A chromosome segment substituted line (CSSL) represents an ideal resource for studying quantitative traits like thermotolerance. To develop wheat inter-varietal CSSLs with E6015-3S (a heat-sensitive genotype) being the recipient parent, genome-wide unique DNA markers are urgently needed for marker-assisted selection. In this study, 11,016 primer pairs targeting 5036 indel sites were successfully designed for E6015-3S, with an average density of 0.36 indels per Mbp. These primer pairs are believed to be unique and polymorphic in the wheat genome; as gathered from the evidence, (i) 76.18 to 99.34% of the 11,016 primer pairs yielded a single hit during sequence alignment with 18 sequenced genomes, (ii) 83.59 to 90.98% of 1042 synthesized primer pairs amplified a single band in 16 wheat accessions, and (iii) 59.69 to 99.81% of the tested 1042 primer pairs were polymorphic between E6015-3S and 15 individual wheat accessions. These primer pairs are also anticipated with excellent resolvability on agarose or polyacrylamide gels, since most of them have indel sizes from 15 to 46 bp, amplicon sizes from 141 to 250 bp, and polymorphism ratios from 6.0 to 25.0%. Collectively, these primer pairs are ideal DNA markers for inter-varietal CSSL development and more broad applications, like germplasm classification, seed purity testing, genetic linkage mapping, and marker-assisted breeding in wheat, owing to their uniqueness, polymorphism, and easy-to-use characteristics. Full article

The whiteness of rice grains (WRG) is a key indicator of appearance quality, directly impacting its commercial value. The trait is quantitative, influenced by multiple factors, and no specific genes have been cloned to date. In this study, we first examined the correlation between the whiteness of polished rice, cooked rice, and rice flour, finding that the whiteness of rice flour significantly correlated with both polished and cooked rice. Thus, the whiteness of rice flour was chosen as the indicator of WRG in our QTL analysis. Using a set of chromosome segment substitution lines (CSSL) with japonica rice Koshihikari as the recipient and indica rice Nona Bokra as the donor, we analyzed QTLs for WRG across two growth environments and identified six WRG QTLs. Notably, qWRG9 on chromosome 9 displayed stable genetic effects in both environments. Through chromosomal segment overlapping mapping, qWRG9 was narrowed to a 1.2 Mb region. Additionally, a BC₄F₂ segregating population confirmed that low WRG was a dominant trait governed by the major QTL qWRG9, with a segregation ratio of low to high WRG approximating 3:1, consistent with Mendelian inheritance. Further grain quality analysis on the BC₄F₂ population revealed that rice grains carrying the Indica-type qWRG9 allele not only exhibited lower WRG but also had significantly higher protein content. These findings support the fine mapping of the candidate gene and provide an important QTL for improving rice grain quality through genetic improvement. Full article

A narrow genetic basis limits further the improvement of modern Gossypium hirsutum cultivar. The abundant genetic diversity of wild species provides available resources to solve this dilemma. In the present study, a chromosome segment substitution line (CSSL) population including 553 individuals was established using G. darwinii accession 5-7 as the donor parent and G. hirsutum cultivar CCRI35 as the recipient parent. After constructing a high-density genetic map with the BC₁ population, the genotype and phenotype of the CSSL population were investigated. A total of 235 QTLs, including 104 QTLs for fiber-related traits and 132 QTLs for seed-related traits, were identified from four environments. Among these QTLs, twenty-seven QTLs were identified in two or more environments, and twenty-five QTL clusters consisted of 114 QTLs. Moreover, we identified three candidate genes for three stable QTLs, including GH_A01G1096 (ARF5) and GH_A10G0141 (PDF2) for lint percentage, and GH_D01G0047 (KCS4) for seed index or oil content. These results pave way for understanding the molecular regulatory mechanism of fiber and seed development and would provide valuable information for marker-assisted genetic improvement in cotton. Full article

Fiber length (FL) and strength (FS) are the core indicators for evaluating cotton fiber quality. The corresponding stages of fiber elongation and secondary wall thickening are of great significance in determining FL and FS formation, respectively. QTL mapping and high-throughput sequencing technology have been applied to dissect the molecular mechanism of fiber development. In this study, 15 cotton chromosome segment substitution lines (CSSLs) with significant differences in FL and FS, together with their recurrent parental Gossypium hirsutum line CCRI45 and donor parent G. barbadense line Hai1, were chosen to conduct RNA-seq on developing fiber samples at 10 days post anthesis (DPA) and 20 DPA. Differentially expressed genes (DEGs) were obtained via pairwise comparisons among all 24 samples (each one with three biological repeats). A total of 969 DEGs related to FL-high, 1285 DEGs to FS-high, and 997 DEGs to FQ-high were identified. The functional enrichment analyses of them indicated that the GO terms of cell wall structure and ROS, carbohydrate, and phenylpropanoid metabolism were significantly enriched, while the GO terms of glucose and polysaccharide biosynthesis, and brassinosteroid and glycosylphosphatidylinositol metabolism could make great contributions to FL and FS formation, respectively. Weighted gene co-expressed network analyses (WGCNA) were separately conducted for analyzing FL and FS traits, and their corresponding hub DEGs were screened in significantly correlated expression modules, such as EXPA8, XTH, and HMA in the fiber elongation and WRKY, TDT, and RAC-like 2 during secondary wall thickening. An integrated analysis of these hub DEGs with previous QTL identification results successfully identified a total of 33 candidate introgressive DEGs with non-synonymous mutations between the Gh and Gb species. A common DEG encoding receptor-like protein kinase 1 was reported to likely participate in fiber secondary cell thickening regulation by brassionsteroid signaling. Such valuable information was conducive to enlightening the developing mechanism of cotton fiber and also provided an abundant gene pool for further molecular breeding. Full article

The tiller angle, which is an important agronomic trait, determines plant architecture and greatly influences the grain yield of rice. In this study, a population of chromosome segment substitution lines derived from a cross between a japonica variety with a compact plant architecture—Koshihikari—and an indica variety with a spread-out plant architecture—Nona Bokra—was used to investigate the genetic basis of the tiller angle. Five quantitative trait loci (qTA1, qTA5, qTA9-1, qTA9-2, and qTA11) for the tiller angle were detected on chromosomes 1, 5, 9, 9, and 11 in two different environments. The phenotypic variation in these QTLs ranged from 3.78% to 8.22%. Two pairs of digenic epistatic QTLs were detected in Lingshui. The epistatic interaction explained 15.19% and 13.60% of the phenotypic variance, respectively. Among the five QTLs, qTA9-2 was detected in both environments. An F₂ mapping population containing the qTA9-2 QTL was established. The location of qTA9-2 was narrowed down to a 187 kb region between InDel markers M9 and M10 on chromosome 9. Thirty open reading frames (ORFs), including TAC1, a gene known to regulate the tiller angle, were identified in this region. The gene sequencing results suggested that a base substitution from G to A at position 1557 in the 3′-untranslated region led to a difference in the expression of qTA9-2 in Koshihikari and Nona Bokra. These findings provide a potential gene resource for the improvement of rice plant architecture. Full article