Fine mapping and cloning of the major seed protein quantitative trait loci on soybean chromosome 20.
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ABSTRACT:
SUBMITTER: Fliege CE
PROVIDER: S-EPMC9303569 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Key messageFour major quantitative trait loci for 100-seed weight were identified in a soybean RIL population under five environments, and the most likely candidate genes underlying these loci were identified. Seed weight is an important target of soybean breeding. However, the genes underlying the major quantitative trait loci (QTL) controlling seed weight remain largely unknown. In this study, a soybean population of 300 recombinant inbred lines (RILs) derived from a cross between PI595843 (PI) and WH was used to map the QTL and identify candidate genes for seed weight. The RIL population was genotyped through whole genome resequencing, and phenotyped for 100-seed weight under five environments. A total of 38 QTL were detected, and four major QTL, each explained at least 10% of the variation in 100-seed weight, were identified. Six candidate genes within these four major QTL regions were identified by analyses of their tissue expression patterns, gene annotations, and differential gene expression levels in soybean seeds during four developmental stages between two parental lines. Further sequence variation analyses revealed a C to T substitution in the first exon of the Glyma.19G143300, resulting in an amino acid change between PI and WH, and thus leading to a different predicted kinase domain, which might affect its protein function. Glyma.19G143300 is highly expressed in soybean seeds and encodes a leucine-rich repeat receptor-like protein kinase (LRR-RLK). Its predicted protein has typical domains of LRR-RLK family, and phylogenetic analyses reveled its similarity with the known LRR-RLK protein XIAO (LOC_Os04g48760), which is involved in controlling seed size. The major QTL and candidate genes identified in this study provide useful information for molecular breeding of new soybean cultivars with desirable seed weight.
| S-EPMC9870841 | biostudies-literature
Project description:Chalkiness is a crucial determinant of rice quality. During seed filling period, high temperature usually increases grain chalkiness, resulting in poor grain quality. Rice chalkiness was controlled by quantitative trait loci (QTLs) and influenced by environmental conditions. In this study, we identified two single-segment substitution lines (SSSLs) 22-05 and 15-06 with significantly lower percentage of grain chalkiness (PGC) than recipient Huajingxian 74 (HJX74) over 6 cropping seasons. Two major QTLs for chalkiness, qPGC5 and qPGC6, were located by substitution mapping of SSSLs 22-05 and 15-06, respectively. qPGC5 was located in the 876.5 kb interval of chromosome 5 and qPGC6 was located in the 269.1 kb interval of chromosome 6. Interestingly, the PGC of HJX74 was significantly different between the two cropping seasons per year, with 25.8% in the first cropping season (FCS) and 16.6% in the second cropping season (SCS), while the PGC of SSSLs 22-05 and 15-06 did not significantly differ between FCS and SCS. The additive effects of qPGC5 and qPGC6 on chalkiness in the SSSLs were significantly greater in FCS than in SCS. These results showed that qPGC5 and qPGC6 had major effects on chalkiness and the SSSL alleles were more effective in reducing chalkiness under high temperature condition in FCS. The fine-mapping of the two QTLs will facilitate the cloning of genes for chalkiness and provide new genetic resources to develop new cultivars with low chalkiness even under high temperature condition.
| S-EPMC9280674 | biostudies-literature
Project description:Boiled seed hardness is an important factor in the processing of soybean food products such as nimame and natto. Little information is available on the genetic basis for boiled seed hardness, despite the wide variation in this trait. DNA markers linked to the gene controlling this trait should be useful in soybean breeding programs because of the difficulty of its evaluation. In this report, quantitative trait locus (QTL) analysis was performed to reveal the genetic factors associated with boiled seed hardness using a recombinant inbred line population developed from a cross between two Japanese cultivars, 'Natto-shoryu' and 'Hyoukei-kuro 3', which differ largely in boiled seed hardness, which in 'Natto-shoryu' is about twice that of 'Hyoukei-kuro 3'. Two significantly stable QTLs, qHbs3-1 and qHbs6-1, were identified on chromosomes 3 and 6, for which the 'Hyoukei-kuro 3' alleles contribute to decrease boiled seed hardness for both QTLs. qHbs3-1 also showed significant effects in progeny of a residual heterozygous line and in a different segregating population. Given its substantial effect on boiled seed hardness, SSR markers closely linked to qHbs3-1, such as BARCSOYSSR_03_0165 and BARCSOYSSR_03_0185, could be useful for marker-assisted selection in soybean breeding.
| S-EPMC4267311 | biostudies-literature
Project description:Flowering time is a major adaptive trait in plants and an important selection criterion for crop species. In maize, however, little is known about its molecular basis. In this study, we report the fine mapping and characterization of a major quantitative trait locus located on maize chromosome 10, which regulates flowering time through photoperiod sensitivity. This study was performed in near-isogenic material derived from a cross between the day-neutral European flint inbred line FV286 and the tropical short-day inbred line FV331. Recombinant individuals were identified among a large segregating population and their progenies were scored for flowering time. Combined genotypic characterization led to delimit the QTL to an interval of 170 kb and highlighted an unbalanced recombination pattern. Two bacterial artificial chromosomes (BACs) covering the region were analyzed to identify putative candidate genes, and synteny with rice, sorghum, and brachypodium was investigated. A gene encoding a CCT domain protein homologous to the rice Ghd7 heading date regulator was identified, but its causative role was not demonstrated and deserves further analyses. Finally, an association study showed a strong level of linkage disequilibrium over the region and highlighted haplotypes that could provide useful information for the exploitation of genetic resources and marker-assisted selection in maize.
| S-EPMC2787439 | biostudies-literature
Project description:Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits. To date, a total of 313 QTL for 31 quantitative traits have been reported in 14 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, the scaffold sequences, or the pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but the most used ones were simple sequence repeats (SSRs) or single nucleotide polymorphisms (SNPs). To uniquely map the SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules, methods with several scripts and database files were developed to locate PCR- and SNP-based markers onto the same reference, co-locate QTL, and scan genome-wide candidate genes. Using these methods, 195 out of 200 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters; the candidate genes that co-located with these QTL clusters were also predicted. The methods and tools presented in this article facilitate marker re-mapping to a new reference, genome-wide QTL analysis, candidate gene scanning, and breeding applications in flax and other crops.
| S-EPMC7359702 | biostudies-literature
Project description:In soybean [Glycine max (L.) Merrill], the genetic analysis of seed yield is important to aid in the breeding of high-yielding cultivars. Seed yield is a complex trait, and the number of quantitative trait loci (QTL) involved in seed yield is high. The aims of this study were to identify QTL associated with seed yield and validate their effects on seed yield using near-isogenic lines. The QTL analysis was conducted using a recombinant inbred line population derived from a cross between Japanese cultivars 'Toyoharuka' and 'Toyomusume', and eight seed yield-associated QTL were identified. There were significant positive correlations between seed yield and the number of favorable alleles at QTL associated with seed yield in the recombinant inbred lines for three years. The effects of qSY8-1, a QTL promoting greater seed yield, was validated in the Toyoharuka background. In a two-year yield trial, the 100-seed weight and seed yield of Toyoharuka-NIL, the near-isogenic line having the Toyomusume allele at qSY8-1, were significantly greater than those of Toyoharuka (106% and 107%, respectively) without any change for days to flowering and maturity. Our results suggest that qSY8-1 was not associated with maturity genes, and contributed to the 100-seed weight.
| S-EPMC8573547 | biostudies-literature
Project description:Pythium root rot is one of the significant diseases of soybean (Glycine max (L.) Merr.) in the United States. The causal agent of the disease is a soil-borne oomycete pathogen Pythium irregulare, the most prevalent and aggressive species of Pythium in North Central United States. However, few studies have been conducted in soybean for the identification of quantitative trait loci (QTL) for tolerance to P. irregulare In this study, two recombinant inbred line (RIL) populations (designated as POP1 and POP2) were challenged with P. irregulare (isolate CMISO2-5-14) in a greenhouse assay. POP1 and POP2 were derived from 'E09014' × 'E05226-T' and 'E05226-T' × 'E09088', and contained 113 and 79 lines, respectively. Parental tests indicated that 'E05226-T' and 'E09014' were more tolerant than 'E09088', while 'E09088' was highly susceptible to the pathogen. The disease indices, root weight of inoculation (RWI) and ratio of root weight (RRW) of both populations showed near normal distributions, with transgressive segregation, suggesting the involvement of multiple QTL from both parents contributed to the tolerance. All the lines were genotyped using Illumina Infinium BARCSoySNP6K iSelect BeadChip and yielded 1373 and 1384 polymorphic markers for POP1 and POP2, respectively. Notably, despite high density, polymorphic markers coverage was incomplete in some genomic regions. As such, 28 and 37 linkage groups were obtained in POP1 and POP2, respectively corresponding to the 20 soybean chromosomes. Using RRW, one QTL was identified in POP1 on Chromosome 20 that explained 12.7-13.3% of phenotypic variation. The desirable allele of this QTL was from 'E05226-T'. Another QTL was found in POP2 on Chromosome 11. It explained 15.4% of the phenotypic variation and the desirable allele was from 'E09088'. However, no QTL were identified using RWI in either population. These results supported that RRW was more suitable to be used to evaluate P. irregulare tolerance in soybean.
| S-EPMC6169387 | biostudies-other
Project description:Prior studies with crosses of the FVB/NJ (FVB; seizure-induced cell death-susceptible) mouse and the C57BL/6J (B6; seizure-induced cell death-resistant) mouse revealed the presence of a quantitative trait locus (QTL) on chromosome 15 that influenced susceptibility to kainic acid-induced cell death (Sicd2). In an earlier study, we confirmed that the Sicd2 interval harbors gene(s) conferring strong protection against seizure-induced cell death through the creation of the FVB.B6-Sicd2 congenic strain, and created three interval-specific congenic lines (ISCLs) that encompass Sicd2 on chromosome 15 to fine-map this locus. To further localise this Sicd2 QTL, an additional congenic line carrying overlapping intervals of the B6 segment was created (ISCL-4), and compared with the previously created ISCL-1-ISCL-3 and assessed for seizure-induced cell death phenotype. Whereas all of the ISCLs showed reduced cell death associated with the B6 phenotype, ISCL-4, showed the most extensive reduction in seizure-induced cell death throughout all hippocampal subfields. In order to characterise the susceptibility loci on Sicd2 by use of this ISCL and identify compelling candidate genes, we undertook an integrative genomic strategy of comparing exon transcript abundance in the hippocampus of this newly developed chromosome 15 subcongenic line (ISCL-4) and FVB-like littermates. We identified 10 putative candidate genes that are alternatively spliced between the strains and may govern strain-dependent differences in susceptibility to seizure-induced excitotoxic cell death. These results illustrate the importance of identifying transcriptomics variants in expression studies, and implicate novel candidate genes conferring susceptibility to seizure-induced cell death.
| S-EPMC3883458 | biostudies-literature
Project description:BackgroundSingle nucleotide polymorphisms (SNPs) which capture a significant impact on a trait can be identified with genome-wide association studies. High linkage disequilibrium (LD) among SNPs makes it difficult to identify causative variants correctly. Thus, often target regions instead of single SNPs are reported. Sample size has not only a crucial impact on the precision of parameter estimates, it also ensures that a desired level of statistical power can be reached. We study the design of experiments for fine-mapping of signals of a quantitative trait locus in such a target region.MethodsA multi-locus model allows to identify causative variants simultaneously, to state their positions more precisely and to account for existing dependencies. Based on the commonly applied SNP-BLUP approach, we determine the z-score statistic for locally testing non-zero SNP effects and investigate its distribution under the alternative hypothesis. This quantity employs the theoretical instead of observed dependence between SNPs; it can be set up as a function of paternal and maternal LD for any given population structure.ResultsWe simulated multiple paternal half-sib families and considered a target region of 1 Mbp. A bimodal distribution of estimated sample size was observed, particularly if more than two causative variants were assumed. The median of estimates constituted the final proposal of optimal sample size; it was consistently less than sample size estimated from single-SNP investigation which was used as a baseline approach. The second mode pointed to inflated sample sizes and could be explained by blocks of varying linkage phases leading to negative correlations between SNPs. Optimal sample size increased almost linearly with number of signals to be identified but depended much stronger on the assumption on heritability. For instance, three times as many samples were required if heritability was 0.1 compared to 0.3. An R package is provided that comprises all required tools.ConclusionsOur approach incorporates information about the population structure into the design of experiments. Compared to a conventional method, this leads to a reduced estimate of sample size enabling the resource-saving design of future experiments for fine-mapping of candidate variants.
| S-EPMC7324978 | biostudies-literature
Project description:BACKGROUND:Deciphering the genetic basis of prostate cancer aggressiveness could provide valuable information for the screening and treatment of this common but complex disease. We previously detected linkage between a broad region on chromosome 7q22-35 and Gleason score-a strong predictor of prostate cancer aggressiveness. To further clarify this finding and focus on the potentially causative gene, we undertook a fine-mapping study across the 7q22-35 region. METHODS:Our study population encompassed 698 siblings diagnosed with prostate cancer. 3,072 single nucleotide polymorphisms (SNPs) spanning the chromosome 7q22-35 region were genotyped using the Illumina GoldenGate assay. The impact of SNPs on Gleason scores were evaluated using affected sibling pair linkage and family-based association tests. RESULTS:We confirmed the previous linkage signal and narrowed the 7q22-35 prostate cancer aggressiveness locus to a 370?kb region. Centered under the linkage peak is the gene KLRG2 (killer cell lectin-like receptor subfamily G, member 2). Association tests indicated that the potentially functional non-synonymous SNP rs17160911 in KLRG2 was significantly associated with Gleason score (P?=?0.0007). CONCLUSIONS:These findings suggest that genetic variants in the gene KLRG2 may affect Gleason score at diagnosis and hence the aggressiveness of prostate cancer.
| S-EPMC3027848 | biostudies-literature