Abstract:Leaf area, length and width affect the photosynthetic capability of a plant and so increasing the photosynthetic rate per unit leaf area may improve seed yield in soybean. In this study, simple sequence repeat (SSR) markers were used to identify the genomic regions significantly associated with the quantitative trait locus (QTL) that controls length, width and the length/width ratio of the terminal and lateral leaflet in two segregating F 2:10 recombinant inbred line (RIL) populations, ÔKeounolkongÕ · ÔShinpal… Show more
“…qLT19Z-2 and qLT19G-2 are two important QTL hotspots correlated to leaf type traits identified in the genetic intervals on the posterior part of chromosome 19. As is shown in (Additional file 1: Table S18), a number of previously published QTLs for leaf type and yield-related traits clustered in the hereditary blocks of qLT19Z-2 and qLT19G-2 [25, 31, 34, 35, 38, 48–62]. Comparably, qLT4Z-1 and qLT4G-2 were novel QTL hotspots on chromosome 04 for leaf type traits in the current study.…”
Background
The different leaf type associated traits of soybean (
Glycine max
L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to identify quantitative trait loci (QTLs) affecting leaf type traits, two advanced recombinant inbred line (RIL, ZH, Zhonghuang 24 × Huaxia 3; GB, Guizao 1 × Brazil 13) populations were introduced to score phenotypic values in plants across nine different environments (years, seasons, locations and soybean growth stages). Two restriction site-associated DNA sequencing (RAD-seq) based high-density genetic linkage maps with an average distance of 1.00 centimorgan (cM) between adjacent bin markers were utilized for QTL fine mapping.
Results
Correlation analysis showed that most of the traits were correlated with each other and regulated both by hereditary and environmental factors. A total of 190 QTLs were identified for leaf type associated traits in the two populations, of which 14 loci were found to be environmentally stable. Moreover, these detected QTLs were categorized into 34 QTL hotspots, and four important QTL hotspots with phenotypic variance ranging from 3.89–23.13% were highlighted. Furthermore,
Glyma04g05840
,
Glyma19g37820
,
Glyma14g07140
and
Glyma19g39340
were predicted in the intervals of the stable loci and important QTL hotspots for leaf type traits by adopting Gene Ontology (GO) enrichment analysis.
Conclusions
Our findings of the QTLs and the putative genes will be beneficial to gain new insights into the genetic basis for soybean leaf type traits and may further accelerate the breeding process for reasonable leaf type soybean.
Electronic supplementary material
The online version of this article (10.1186/s12864-019-5610-8) contains supplementary material, which is available to authorized users.
“…qLT19Z-2 and qLT19G-2 are two important QTL hotspots correlated to leaf type traits identified in the genetic intervals on the posterior part of chromosome 19. As is shown in (Additional file 1: Table S18), a number of previously published QTLs for leaf type and yield-related traits clustered in the hereditary blocks of qLT19Z-2 and qLT19G-2 [25, 31, 34, 35, 38, 48–62]. Comparably, qLT4Z-1 and qLT4G-2 were novel QTL hotspots on chromosome 04 for leaf type traits in the current study.…”
Background
The different leaf type associated traits of soybean (
Glycine max
L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to identify quantitative trait loci (QTLs) affecting leaf type traits, two advanced recombinant inbred line (RIL, ZH, Zhonghuang 24 × Huaxia 3; GB, Guizao 1 × Brazil 13) populations were introduced to score phenotypic values in plants across nine different environments (years, seasons, locations and soybean growth stages). Two restriction site-associated DNA sequencing (RAD-seq) based high-density genetic linkage maps with an average distance of 1.00 centimorgan (cM) between adjacent bin markers were utilized for QTL fine mapping.
Results
Correlation analysis showed that most of the traits were correlated with each other and regulated both by hereditary and environmental factors. A total of 190 QTLs were identified for leaf type associated traits in the two populations, of which 14 loci were found to be environmentally stable. Moreover, these detected QTLs were categorized into 34 QTL hotspots, and four important QTL hotspots with phenotypic variance ranging from 3.89–23.13% were highlighted. Furthermore,
Glyma04g05840
,
Glyma19g37820
,
Glyma14g07140
and
Glyma19g39340
were predicted in the intervals of the stable loci and important QTL hotspots for leaf type traits by adopting Gene Ontology (GO) enrichment analysis.
Conclusions
Our findings of the QTLs and the putative genes will be beneficial to gain new insights into the genetic basis for soybean leaf type traits and may further accelerate the breeding process for reasonable leaf type soybean.
Electronic supplementary material
The online version of this article (10.1186/s12864-019-5610-8) contains supplementary material, which is available to authorized users.
“…These results suggest that the 12 sub-regions identified on chromosome 16, especially the one described most recently, were acquired more recently in the breeding process. Other studies have described QTLs associated with flowering and maturity [ 54 , 55 ], pod number and quality [ 56 , 57 ], and leaflet format [ 58 ] in these intervals, increasing the possibility of the influence of CNVs on modifications over time. Fig.…”
BackgroundSoybean [Glycine max (L.) Merrill] is one of the most important legumes cultivated worldwide, and Brazil is one of the main producers of this crop. Since the sequencing of its reference genome, interest in structural and allelic variations of cultivated and wild soybean germplasm has grown. To investigate the genetics of the Brazilian soybean germplasm, we selected soybean cultivars based on the year of commercialization, geographical region and maturity group and resequenced their genomes.ResultsWe resequenced the genomes of 28 Brazilian soybean cultivars with an average genome coverage of 14.8X. A total of 5,835,185 single nucleotide polymorphisms (SNPs) and 1,329,844 InDels were identified across the 20 soybean chromosomes, with 541,762 SNPs, 98,922 InDels and 1,093 CNVs that were exclusive to the 28 Brazilian cultivars. In addition, 668 allelic variations of 327 genes were shared among all of the Brazilian cultivars, including genes related to DNA-dependent transcription-elongation, photosynthesis, ATP synthesis-coupled electron transport, cellular respiration, and precursors of metabolite generation and energy. A very homogeneous structure was also observed for the Brazilian soybean germplasm, and we observed 41 regions putatively influenced by positive selection. Finally, we detected 3,880 regions with copy-number variations (CNVs) that could help to explain the divergence among the accessions evaluated.ConclusionsThe large number of allelic and structural variations identified in this study can be used in marker-assisted selection programs to detect unique SNPs for cultivar fingerprinting. The results presented here suggest that despite the diversification of modern Brazilian cultivars, the soybean germplasm remains very narrow because of the large number of genome regions that exhibit low diversity. These results emphasize the need to introduce new alleles to increase the genetic diversity of the Brazilian germplasm.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2431-x) contains supplementary material, which is available to authorized users.
“…21 detected a QTL related to leaflet length (7,922,227–41,622,802 bp) was located near qCLN14-100 and qLDWR14-95 (7,440,291–8,071,592 bp) on Chr14, while Kim et al . 15 identified two QTLs related to leaflet shape and width (13,755,345–17,021,739 bp) were located near qTLA15-99 and qLDW15-98 (12,793,197–15,034,369 bp) on Chr15. Reinprecht et al .…”
Section: Discussionmentioning
confidence: 96%
“…Kim et al . 15 identified 7 QTLs for leaflet length and width in two F 2:10 populations. The QTLs of leaf traits associated with shading were relatively few.…”
Soybean (
Glycine max
L.) is an important food and oil crop widely planted by intercropping in southwest China. The shade caused by intercropping changes plant growth traits, such as soybean leaf and dry mass, thereby reducing yields. To improve the yield and elucidate the genetic mechanism of the leaf-related traits in intercropped soybeans, we measured the F
6:7–8
recombinant inbred lines (RILs) derived from the cross of ‘Nandou 12’ and ‘Jiuyuehuang’ for six leaf-related traits under monoculture and relay intercropping in 2015 and 2016. We found 6366 single-nucleotide polymorphisms (SNPs) markers that covered the whole genome of soybean distributed in 20 linkage groups, which spanned 2818.67 cM with an average interval of 0.44 cM between adjacent markers. Nineteen quantitative trait loci (QTLs) were detected in two environments in 2 years. Three candidate genes associated to leaf-related traits were found according to gene expression and GO enrichment analyses. These results revealed the susceptibility of leaf phenotype to shading and helped elucidate the mechanisms that control leaf-related traits.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
