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(A) Gene location vs. expression quantitative trait loci (eQTL) genetic location scatter plot of eQTL for genes annotating to the flavonoid biosynthesis pathway. Eight genes involved in flavonoid biosynthesis, particularly chalcone synthase (CHS) genes, mapped to the chromosome (Chr) 8 locus ~904 cM. The Chr 8 cis-acting eQTL for CHS1 was identified at the Inhibitor locus for seed coat color. Each eQTL point is color-coded to represent transcript accumulation upregulated by the Minsoy (red) allele or the Noir 1 (blue) allele. (B) The seed coat pigmentation QTL maps to Chr 8 and colocalizes with the flavonoid biosynthesis eQTL hotspot.
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The complex network of regulatory factors and interactions involved in transcriptional regulation within the seed is not well understood. To evaluate gene expression regulation in the immature seed, we utilized a genetical genomics approach on a soybean [Glycine max (L.) Merr.] recombinant inbred line (RIL) population and produced a genome-wide exp...
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... flavonoid biosynthesis pathway takes place in the immature seed. Upon mining the eQTL dataset for all genes that annotate to the flavonoid biosynthesis pathway Gene Ontology cat- egory, we found that >20% of the eQTL identified for genes in this pathway (adjusted P value = 2.06´1006´06´10 -4 ) mapped to a Chr 8 interval (~904 total cM, Fig. 2A, Suppl. Table S6). Moreover, the eQTL for flavonoid biosynthesis pathway genes all possessed additive effects with the Noir 1 allele, the genotype with black (versus yellow) seed color. Of these genes, the eQTL for only one gene candidate, the CHS1 gene (Glyma08g11610), was identified as a cis-acting regulator. Using a quantitative ...
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... (Glyma08g11610), was identified as a cis-acting regulator. Using a quantitative measurement of seed coat pigmenta- tion and the genetic map assembled for the M ´ N RIL population, a seed coat pigmentation QTL was also identi- fied over the Chr 8 interval (Suppl . Table S3) and accounted for over 77% of the seed coat pigmentation trait (LOD > 40) (Fig. 2B). The position of this seed coat pigmentation QTL is consistent with the genomic location of a repetitive cluster of CHS genes that controls seed coat pigmentation through generation of small RNAs that downregulate all CHS gene family members ( Tuteja et al., ...
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... Table S7). Clusters of seed- specific gene eQTL were found at hotspots on Chr 20 (2498 total cM, Fig. 3A) and Chr 13 (1627 total cM, Fig. 3A). The location of these seed-specific eQTL hotspots did not cor- respond to the eQTL hotspot with the greatest number of eQTL (Chr 7, Fig. 1B) or to the eQTL hotspot for flavonoid biosynthesis (Chr 8, Fig. ...
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... eQTL hotspot (2498 total cM) on Chr 20 were examined for enrichment in spe- cific functional categories. Based on Gene Ontology anno- tations, the most highly enriched categories at the Chr 20 hotspot were for photosynthesis (adjusted P value = 4.65´1065´ 65´10 -16 ) and fatty acid biosynthetic process (adjusted P value = 7.1 ´ 10 -8 ) (Suppl. Fig. S2). The eQTL for all genes with either photosynthesis or fatty acid biosynthetic process annota- tions were subsequently highlighted. Photosynthesis gene eQTL were found to cluster to three regions of the genome, including hotspots on Chr 7, 20, and 13 (Fig. 3B, Suppl. Table S8). Hotspots for eQTL of fatty acid biosynthesis genes were ...
Citations
... Identification of consistent eQTLs, which at times were not the same markers but a marker in LD with the markers initially showed association with an e-trait, indicated the successful use of a manageable population for such a study. Expression QTL analysis was successfully applied in many crop plants earlier [57][58][59][60][61][62][63][64][65][66], but mostly using bi-parental populations or largely in diploid organisms. Hence, this study presents precedence to perform it in a polyploid crop and for the gene(s) of interest, not the whole transcriptome making it more affordable. ...
Cotton (Gossypium spp.) is the primary source of natural textile fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an Upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time, and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified molecular markers associated with the gene expression traits via genome-wide association analysis using a 63 K SNP Array. Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed associations with expression traits. Of these 396 markers, 159 were mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated.
... The candidate genes associated with fatty acid content in mature soybean seeds that were detected in this study have been previously examined. Bolon, Hyten, Orf, Vance, & Muehlbauer (2014) used a genetical genomics approach to investigate a soybean RIL population, and produced a genome-wide expression quantitative trait locus (eQTL) dataset. The eQTL in which the candidate gene ...
Seed fatty acid content is an important consideration for soybean produced for food, feed, and industrial applications. In this study, MCScanX was used to analyze the entire soybean genome to generate a collinearity block, which was then used to assess the collinearity among the soybean fatty acid quantitative trait loci (QTL) in the SoyBase database. The hub‐QTLs located in the Gm06, Gm07, and Gm10 segments were identified. The Kyoto Encyclopedia of Genes and Genomes and gene ontology databases were used to analyze the genes in hub‐QTL regions, resulting in the identification of 17 candidate genes related to soybean fatty acid content. Two lines with different fatty acid contents and a recurrent parent were selected from a chromosome segment substitution line library for a subsequent quantitative real‐time polymerase chain reaction (qRT‐PCR) assay to verify the candidate gene expression patterns. Four genes were related to the total soybean fatty acid content, while three genes were related to the content of specific fatty acid types. The results of this study may be relevant for the fine mapping of soybean fatty acid QTLs/genes.
... Our GWAS study across multiple environments allowed us to identify a new environmentally stable QTL, GqOil20, and an underlying candidate gene, GmOLEO1 that is capable of increasing seed oil content in soybean. Notably, the GmOLEO1 locus was previously identified as a possible candidate for an eQTL associated with seed oil accumulation [34], and it is physically close to other oil-related QTLs previously identified by linkage mapping [21][22][23]. GmOLEO1 may have been identified in this study because the corresponding alleles were fixed with respect to oil variation during domestication. ...
Increasing seed oil content is one of the most important breeding goals for soybean due to a high global demand for edible vegetable oil. However, genetic improvement of seed oil content has been difficult in soybean because of the complexity of oil metabolism. Determining the major variants and molecular mechanisms conferring oil accumulation is critical for substantial oil enhancement in soybean and other oilseed crops. In this study, we evaluated the seed oil contents of 219 diverse soybean accessions across six different environments and dissected the underlying mechanism using a high-resolution genome-wide association study (GWAS). An environmentally stable quantitative trait locus (QTL), GqOil20, significantly associated with oil content was identified, accounting for 23.70% of the total phenotypic variance of seed oil across multiple environments. Haplotype and expression analyses indicate that an oleosin protein-encoding gene (GmOLEO1), colocated with a leading single nucleotide polymorphism (SNP) from the GWAS, was significantly correlated with seed oil content. GmOLEO1 is predominantly expressed during seed maturation, and GmOLEO1 is localized to accumulated oil bodies (OBs) in maturing seeds. Overexpression of GmOLEO1 significantly enriched smaller OBs and increased seed oil content by 10.6% compared with those of control seeds. A time-course transcriptomics analysis between transgenic and control soybeans indicated that GmOLEO1 positively enhanced oil accumulation by affecting triacylglycerol metabolism. Our results also showed that strong artificial selection had occurred in the promoter region of GmOLEO1, which resulted in its high expression in cultivated soybean relative to wild soybean, leading to increased seed oil accumulation. The GmOLEO1 locus may serve as a direct target for both genetic engineering and selection for soybean oil improvement.
... This technique could be especially important in triticale to understand the biological and genetic processes happening in the development of the hybrid by revealing the gene regulatory network of the whole genome. Expression QTLs were reported in several species, including barley, soybean, and rice (Chen et al., 2010;Bolon et al., 2014;Wang et al., 2014;Kuroha et al., 2017), unraveling gene regulatory networks. ...
Triticale (×Triticosecale Wittmack) is a man-made species developed by crossing wheat (Triticum spp.) and rye (Secale cereale L.). It incorporates favorable alleles from both progenitor species (wheat and rye), enabling adaptation to environments that are less favorable for wheat yet providing better biomass yield and forage quality. Triticale has huge potential for both grain and forage production, though research to improve the crop for better adaptation and grain quality is lagging behind that of other small grains. It is also gaining popularity as a cover crop to improve soil health and reduce nutrient leaching. Because of its genetic and flower structure, triticale is suitable for both line and hybrid breeding methods. Advances in the areas of molecular biology and the wealth of genomic resources from both wheat and rye can be exploited for triticale improvement. Gene mapping and genomic selection will facilitate triticale breeding by increasing selection precision and reducing time and cost. The objectives of this review are to summarize current triticale production status, breeding, and genetics research achievements and to highlight gaps for future research.
... Progress in the acquisition of large-scale transcriptome data has greatly facilitated expression QTL (eQTL) analysis (Jansen and Nap, 2001;Kliebenstein, 2009;Druka et al., 2010;Cubillos et al., 2012a;Chitwood and Sinha, 2013); the gene expression level is considered a trait (expression trait or e-trait). eQTL studies of the model plant Arabidopsis thaliana (Decook et al., 2006;Kliebenstein et al., 2006;Keurentjes et al., 2007;West et al., 2007;Burow et al., 2009;Jimenez-Gomez et al., 2010;Cubillos et al., 2012b;Lowry et al., 2013), of crops (Potokina et al., 2008;Swanson-Wagner et al., 2009;Chen et al., 2010;Holloway et al., 2011;Bolon et al., 2014;Wang Y. et al., 2014;Ranjan et al., 2016), and of trees (Drost et al., 2010(Drost et al., , 2015 mapped expression variations to both cis-and trans-acting regulatory polymorphisms: cis-eQTL (DNA polymorphisms within or close to the gene) and trans-eQTL (polymorphisms located anywhere in the genome). In rice, Wang et al. (2010) performed eQTL mapping of recombinant inbred lines (RILs) derived from two indica varieties, Zhenshan 97 and Minghui 63, to identify gene regulatory networks that contribute to an agriculturally important trait. ...
To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua). After evaluating the phenotypic response of the RILs exposed to submergence, confirming the genotypes of the populations, and generating 188 genetic markers, we identified 10,047 significant eQTLs comprised of 2,902 cis-eQTLs and 7,145 trans-eQTLs and three significant eQTL hotspots on chromosomes 1, 4, and 12 that affect the expression of many genes. The hotspots on chromosomes 1 and 4 located at different position from phQTLs detected in this study and other previous studies. We then regarded the eQTL hotspots as key regulatory points to infer causal regulatory networks of deepwater response including rapid internode elongation. Our results suggest that the downstream regulation of the eQTL hotspots on chromosomes 1 and 4 is independent, and that the target genes are partially regulated by SNORKEL1 and SNORKEL2 genes (SK1/2), key ethylene response factors. Subsequent bioinformatic analyses, including gene ontology-based annotation and functional enrichment analysis and promoter enrichment analysis, contribute to enhance our understanding of SK1/2-dependent and independent pathways. One remarkable observation is that the functional categories related to photosynthesis and light signaling are significantly over-represented in the candidate target genes of SK1/2. The combined results of these investigations together with genetical genomics approaches using structured populations with a deepwater response are also discussed in the context of current molecular models concerning the rapid internode elongation in deepwater rice. This study provides new insights into the underlying genetic architecture of gene expression regulating the response to flooding in deepwater rice and will be an important community resource for analyses on the genetic basis of deepwater responses.
... Of the 134 trait-associated CDGs, 29 overlapped with previous CDGs, 11 were exactly the same as candidate genes in previous trait association studies, and 66 were covered by previous domesticated and improved quantitative trait loci or their adjacent regions (Table 2 and Supplemental Table S12). Among the 29, 11, and 66 CDGs, six were common (Table 2), including the SOC gene Glyma20 g10240 (Zhou et al., 2015a), the SS gene Glyma08 g09310 (Bolon et al., 2014), the alkaline-salt tolerance (AST) gene Glyma05 g06070 (Mochida et al., 2010), and the FT genes Glyma14 g16040 and Glyma15 g17480 (Jung et al., 2012;Kim et al., 2012b;Xue et al., 2012;Chung et al., 2014;Zhou et al., 2015b) (Table 2). More importantly, Glyma15 g17480 (GmZTL3) has been functionally characterized in soybean (Xue et al., 2012). ...
Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontol-ogy (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 trait-associated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies , and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 (GmZTL3). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition , eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research. D uring the approximate 10,000-yr period of domes-tication, many morphological and physiological traits in wild species of plants and animals have undergone dramatic modification to meet human needs. In plants, these traits include more or larger seeds, reduced seed dispersal, more robust plants, and decreased chemical and morphological defenses. Studying these domes-tication traits (DTs) is a useful way to identify key genes in their wild ancestors. Extensive studies have been
... Of the 134 trait-associated CDGs, 29 overlapped with previous CDGs, 11 were exactly the same as candidate genes in previous trait association studies, and 66 were covered by previous domesticated and improved quantitative trait loci or their adjacent regions (Table 2 and Supplemental Table S12). Among the 29, 11, and 66 CDGs, six were common (Table 2), including the SOC gene Glyma20 g10240 (Zhou et al., 2015a), the SS gene Glyma08 g09310 (Bolon et al., 2014), the alkaline-salt tolerance (AST) gene Glyma05 g06070 (Mochida et al., 2010), and the FT genes Glyma14 g16040 and Glyma15 g17480 (Jung et al., 2012;Kim et al., 2012b;Xue et al., 2012;Chung et al., 2014;Zhou et al., 2015b) (Table 2). More importantly, Glyma15 g17480 (GmZTL3) has been functionally characterized in soybean (Xue et al., 2012). ...
Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 traitassociated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 (GmZTL3). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.
... In addition, human eQTL studies have shown that loci expected to be involved in selective sweeps are more likely to be eQTLs than other loci (17), allele frequencies of eQTLs that increase expression of a potentially deleterious coding SNP are under stronger purifying selection than those that do not (18), and eQTL allele frequencies within populations are correlated with local adaptation (19,20). To date, eQTL studies in plants have used genetic crosses (21)(22)(23) or species-wide samples (24)(25)(26), making it difficult to distinguish evolutionary forces acting within and between populations. In sum, we currently lack comprehensive tests of selection on within-population eQTLs in any system, especially in plants. ...
Significance
Biologists have long sought to explain why we see genetic variation for traits in populations despite the expectation that selection will remove most variation. We address this question by using gene expression as a model trait and identifying the genetic loci that affect gene expression in a single, large population of the plant Capsella grandiflora . Alleles at loci that affect expression were rarer than expected under neutral expectations, and there was a negative correlation between phenotypic effect size and frequency of these alleles. These observations are consistent with the hypothesis that purifying selection acts on the genetic variation for expression.
... In addition, human eQTL studies have shown that loci expected to be involved in selective sweeps are more likely to be eQTLs than other loci (16) , allele frequencies of eQTLs that increase expression of a potentially deleterious coding SNP are under stronger purifying selection than those that do not (17) , and eQTL allele frequencies within populations are linked to local adaptation (18,19) . To date, eQTL studies in plants have used genetic crosses (20)(21)(22) or species-wide samples (23)(24)(25) , making it difficult to distinguish evolutionary forces acting within and between populations. In sum, we currently lack comprehensive tests of selection on within-population eQTLs in any system, especially in plants. ...
The evolutionary forces that maintain genetic variation for quantitative traits within populations remain poorly understood. One hypothesis suggests that variation is maintained by a balance between new mutations and their removal by selection and drift. Theory predicts that this mutation-selection balance will result in an excess of low-frequency variants and a negative correlation between minor allele frequency and selection coefficients. Here, we test these predictions using the genetic loci associated with total expression variation (eQTLs) and allele-specific expression variation (aseQTLs) mapped within a single population of the plant Capsella grandiflora. In addition to finding eQTLs and aseQTLs for a large fraction of genes, we show that alleles at these loci are rarer than expected and exhibit a negative correlation between phenotypic effect size and frequency. Overall, our results show that the distribution of frequencies and effect sizes of the loci responsible for local expression variation within a single, outcrossing population are consistent with mutation-selection balance.
... Among them, two QTL with main effects, located in Gm05 (soybean chromosome 5, LGA1) and Gm08 (LGA2), respectively, consistently affected isoflavone content across multi-environments [30,35]. Striking eQTL hotspots associated with soybean seed-specific expression on Gm 20, 7, and 13 were discovered by Bolon et al. [38]. Wang et al. [39] identified seven candidate genes on Gm13 (LG F) and assumed Gm13 could be a hotspot of gene cluster that regulated seed isoflavone content. ...
Soybean (Glycine max (L.) Merr.) isoflavone is important for human health and plant defense system. To identify novel quantitative trait loci (QTL) and epistatic QTL underlying isoflavone content in soybean, F5:6, F5:7 and F5:8 populations of 130 recombinant inbred (RI) lines, derived from the cross of soybean cultivar 'Zhong Dou 27' (high isoflavone) and 'Jiu Nong 20' (low isoflavone), were analyzed with 95 new SSR markers. A new linkage map including 194 SSR markers and covering 2,312 cM with mean distance of about 12 cM between markers was constructed. Thirty four QTL for both individual and total seed isoflavone contents of soybean were identified. Six, seven, ten and eleven QTL were associated with daidzein (DZ), glycitein (GC), genistein (GT) and total isoflavone (TI), respectively. Of them 23 QTL were newly identified. The qTIF_1 between Satt423 and Satt569 shared the same marker Satt569 with qDZF_2, qGTF_1 and qTIF_2. The qGTD2_1 between Satt186 and Satt226 was detected in four environments and explained 3.41%-10.98% of the phenotypic variation. The qGTA2_1, overlapped with qGCA2_1 and detected in four environments, was close to the previously identified major QTL for GT, which were responsible for large a effects. QTL (qDZF_2, qGTF_1 and qTIF_2) between Satt144-Satt569 were either clustered or pleiotropic. The qGCM_1, qGTM_1 and qTIM_1 between Satt540-Sat_244 explained 2.02%-9.12% of the phenotypic variation over six environments. Moreover, the qGCE_1 overlapped with qGTE_1 and qTIE_1, the qTIH_2 overlapped with qGTH_1, qGCI_1 overlapped with qDZI_1, qTIL_1 overlapped with qGTL_1, and qTIO_1 overlapped with qGTO_1. In this study, some of unstable QTL were detected in different environments, which were due to weak expression of QTL, QTL by environment interaction in the opposite direction to a effects, and/or epistasis. The markers identified in multi-environments in this study could be applied in the selection of soybean cultivars for higher isoflavone content and in the map-based gene cloning.
