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To keep plant height (PH) stable in various densities, mapping QTL underlying te response of PH to density is of importance for soybean breeding. In this study, two soybean RIL populations were planted under two densities in two environments and PH at the pod-bearing stage (PBS), seed-filling stage (SFS) and maturity stage (MS) were measured to identify QTL controlling PH and its response to density increment. Expression of QTL controlling PH varied due to the change of seeding density, and the response to density (RD) of PH at SFS and MS surpassed that at PBS in both populations. Total 25 PH QTL and 8 RD QTL were identified which functioned on PH at three developmental stages. Of 25 PH QTL, 14, 8 and 8 were detected at PBS, SFS and MS, respectively. Three QTL could be expressed at two stages, and thirteen, seven and six QTL played roles separately at PDS, SFS and MS, respectively. Four QTL were expressed in the two seeding densities, and twelve and ten QTL showed effects specifically at low and high seeding density, respectively. Among eight RD QTL, five, two and one acted on PH at PBS, SFS and MS, and five and three QTL functioned in two environments, respectively. The information found in the present research lays the foundation for molecular design breeding on improving PH with stability in multiple densities in soybean. [ABSTRACT FROM AUTHOR]

Hundred-seed weight (HSW) is an important measure of yield and a useful indicator to monitor the inheritance of quantitative traits affected by genotype and environmental conditions. To identify quantitative trait nucleotides (QTNs) and mine genes useful for breeding high-yielding and high-quality soybean (Glycine max) cultivars, we conducted a multilocus genome-wide association study (GWAS) on HSW of soybean based on phenotypic data from 20 different environments and genotypic data for 109,676 single-nucleotide polymorphisms (SNPs) in 144 four-way recombinant inbred lines. Using five multilocus GWAS methods, we identified 118 QTNs controlling HSW. Among these, 31 common QTNs were detected by various methods or across multiple environments. Pathway analysis identified three potential candidate genes associated with HSW in soybean. We used allele information to study the common QTNs in 20 large-seed and 20 small-seed lines and identified a higher percentage of superior alleles in the large-seed lines than in small-seed lines. These observations will contribute to construct the gene networks controlling HSW in soybean, which can improve the genetic understanding of HSW, and provide assistance for molecular breeding of soybean large-seed varieties. [ABSTRACT FROM AUTHOR]

Soybean varieties suitable for high planting density allow greater yields. However, the seed protein and oil contents, which determine the value of this crop, can be influenced by planting density. Thus, it is important to understand the genetic basis of the responses of different soybean genotypes to planting density. In this study, we quantified the protein and oil contents in a four-way recombinant inbred line (FW-RIL) soybean population under two planting densities and the response to density. We performed quantitative trait locus (QTL) mapping using a single nucleotide polymorphism (SNP) linkage map generated by inclusive composite interval mapping. We identified 14 QTLs for protein content and 17 for oil content at a planting density of 2.15 × 105 plant/ha (D1) and 14 QTLs for protein content and 20 for oil content at a planting density 3.0 × 105 plant/ha (D2). Among the QTLs detected, two oil-content QTLs was detected at both plant densities. In addition, we identified 38 QTLs for the responses of protein and oil contents to planting density. Of the QTLs detected, 70 were identified in previous studies, while 33 were newly identified. Fourty-five QTLs accounted for over 10% of the phenotypic variation of the corresponding trait, based on 23 QTLs at a marker interval distance of ~600 kb detected under different densities and with the responses to density difference. Pathway analysis revealed four candidate genes involved in protein and oil biosynthesis/metabolism. These results improve our understanding of the genetic underpinnings of protein and oil biosynthesis in soybean, laying the foundation for enhancing protein and oil contents and increasing yields in soybean. [ABSTRACT FROM AUTHOR]

Plant height is an important target for soybean breeding. It is a typical quantitative trait controlled by multiple genes and is susceptible to environmental influences. Here, we carried out phenotypic analysis of 156 recombinant inbred lines derived from "Dongnong L13" and "Henong 60" in nine environments at four locations over 6 years using interval mapping and inclusive composite interval mapping methods. We performed quantitative trait locus (QTL) analysis by applying pre-built simple-sequence repeat maps. We detected 48 QTLs, including nine significant QTLs detected by multiple methods and in multiple environments. Meanwhile, genotyping of all lines using the SoySNP660k BeadChip produced 54,836 non-redundant single-nucleotide polymorphism (SNP) genotypes. We used five multi-locus genome-wide association analysis methods to locate 10 quantitative trait nucleotides (QTNs), four of which overlap with previously located QTLs. Five candidate genes related to plant height are predicted to lie within 200 kb of these four QTNs. We identified 19 homologous genes in Arabidopsis, two of which may be associated with plant height. These findings further our understanding of the multi-gene regulatory network and genetic determinants of soybean plant height, which will be important for breeding high-yielding soybean. [ABSTRACT FROM AUTHOR]

Protein content (PC) and oil content (OC) are important breeding traits of soybean [Glycine max (L.) Merr.]. Quantitative trait locus (QTL) mapping for PC and OC is important for molecular breeding in soybean; however, the negative correlation between PC and OC influences the accuracy of QTL mapping. In the current study, a four-way recombinant inbred lines (FW-RILs) population comprising 160 lines derived from the cross (Kenfeng14 × Kenfeng15) × (Heinong48 × Kenfeng19) was planted in eight different environments and PC and OC measured. Conditional and unconditional QTL analyses were carried out by interval mapping (IM) and inclusive complete IM based on linkage maps of 275 simple sequences repeat markers in a FW-RILs population. This analysis revealed 59 unconditional QTLs and 52 conditional QTLs among the FW-RILs. An analysis of additive effects indicated that the effects of 13 protein QTLs were not related to OC, whereas OC affected the expression of 13 and eight QTLs either partially or completely, respectively. Eight QTLs affecting OC were not influenced by PC, whereas six and 26 QTLs were partially and fully affected by PC, respectively. Among the QTLs detected in the current study, two protein QTLs and five oil QTLs had not been previously reported. These findings will facilitate marker-assisted selection and molecular breeding of soybean. [ABSTRACT FROM AUTHOR]

Plant height (PH) is an important trait in soybean, as taller plants may have higher yields but may also be at risk for lodging. Many genes act jointly to influence PH throughout development. To map the quantitative trait loci (QTL) controlling PH, we used the unconditional variable method (UVM) and conditional variable method (CVM) to analyze PH data for a four-way recombinant inbred line (FW-RIL) population derived from the cross of (Kenfeng14 × Kenfeng15) × (Heinong48 × Kenfeng19). We identified 7, 8, 16, 19, 15, 27, 17, 27, 22, and 24 QTL associated with PH at 10 developmental stages, respectively. These QTL mapped to 95 genomic regions. Among these QTL, 9 were detected using UVM and CVM, and 89 and 66 were only detected by UVM or CVM, respectively. In total, 36 QTL controlling PH were detected at multiple developmental stages and these made unequal contributions to genetic variation throughout development. Among 19 novel regions discovered in our study, 7 could explain over 10% of the phenotypic variation and contained only one single QTL. The unconditional and conditional QTL detected here could be used in molecular design breeding across the whole developmental procedure. [ABSTRACT FROM AUTHOR]

Protein content (PC), an important trait in soybean (Glycine max) breeding, is controlled by multiple genes with relatively small effects. To identify the quantitative trait nucleotides (QTNs) controlling PC, we conducted a multi-locus genome-wide association study (GWAS) for PC in 144 four-way recombinant inbred lines (FW-RILs). All the FW-RILs were phenotyped for PC in 20 environments, including four locations over 4 years with different experimental treatments. Meanwhile, all the FW-RILs were genotyped using SoySNP660k BeadChip, producing genotype data for 109,676 non-redundant single-nucleotide polymorphisms. A total of 129 significant QTNs were identified by five multi-locus GWAS methods. Based on the 22 common QTNs detected by multiple GWAS methods or in multiple environments, pathway analysis identified 8 potential candidate genes that are likely to be involved in protein synthesis and metabolism in soybean seeds. Using superior allele information for 22 common QTNs in 22 elite and 7 inferior lines, we found higher superior allele percentages in the elite lines and lower percentages in the inferior lines. These findings will contribute to the discovery of the polygenic networks controlling PC in soybean, increase our understanding of the genetic foundation and regulation of PC, and be useful for molecular breeding of high-protein soybean varieties. [ABSTRACT FROM AUTHOR]

In order to well understand the molecular basis of heterosis in soybean, the methylation-sensitive amplification polymorphism (MSAP) method based on capillary electrophoresis was used to estimate levels and patterns of cytosine methylation in 15-day post-emergence leaves of four parental lines [Jilin 47 (no. 19), EXP (no. 12), Jilin 38 (no. 3) and Yi 3 (no. 6)] and 12 hybrids [Jilin 38 × Yi 3(3 ×  6), Jilin 38 ×  EXP(3 ×  12), Jilin 38 ×  Jilin 47(3 ×  19), Yi 3 ×  Jilin 38(6 ×  3), Yi 3 ×  EXP(6 ×  12), Yi 3 ×  Jilin 47(6 ×  19), EXP × Jilin 38(12 × 3), EXP × Yi 3(12 ×  6), EXP ×  Jilin 47(12 ×  19), Jilin 47 ×  Jilin 38(19 ×  3), Jilin 47 × Yi 3(19 × 6), Jilin 47 × EXP(19 × 12)]. In addition, 12 traits of the hybrids and their parents were also analyzed to understand the relationship between DNA methylation variation and heterosis. MSAP results showed that the total relative methylation level of all hybrids was lower than the corresponding middle parent value, indicating that the methylation degree was decreasing. And may express a variety of genes related to the phenotypic variation of hybridization. Moreover, the hemi-methylation levels of Jilin 38 × Jilin 47 and Yi 3 × Jilin 47 hybrids and full-methylation levels of EXP × Yi 3 and EXP × Jilin 47 hybrids was significant higher than the corresponding mid-parent values. In addition, the heredity of methylation from parents in hybrids is more than the variations, in which there were four types appeared great higher: A1, B4, B8, and D2. Furthermore, the results of relationship between genetic variation in DNA methylation and heterosis showed that the hypo-methylation had a promoting effect to increase node number, and the hype-methylation of hybrids was helpful to add to stem thick. Our results may provide new insights into well understanding the molecular mechanisms of heterosis at the epigenetic level in soybean. [ABSTRACT FROM AUTHOR]