Identification of QTLs Associated with Two-seed Pod Length and Width in Soybean

2021 ◽  
Author(s):  
D.P. Shan ◽  
J.G. Xie ◽  
Y. Yu ◽  
R. Zhou ◽  
Z.L. Cui ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Gene Annotation ◽  
Soybean Seed ◽  
Chromosome 17 ◽  
Substitution Lines ◽  
Epistatic Effects ◽  
Chromosome Segment Substitution Lines ◽  
Trait Locus ◽  
Segment Substitution ◽  
Pod Length

Background: Two-seed pod length and width (TSPL and TSPW, respectively) are the traits underlying seed size, which is an important factor influencing soybean yield. Methods: A population comprising 213 chromosome segment substitution lines from a cross between ‘Suinong14’ (SN14) and ZYD00006 was used for a quantitative trait locus (QTL) analysis. The QTLs were identified on the basis of the phenotypes from 2016 to 2019. Additionally, IciMapping 4.2 was used to analyze the phenotypic and genetic data. Genes were annotated using the KEGG and Phytozome databases. Result: Five QTLs for TSPL and four QTLs for TSPW were identified. One QTL on chromosome 17 was detected for TSPL in 2017 and 2018 as well for TSPW in 2018 and 2019. Analyses of the additive × additive epistatic effects of QTLs revealed six stable loci pairs for epistatic effects on the two traits. On the basis of an alignment of the parental gene sequences and the gene annotation information, Glyma.04G188800, Glyma.11G164700, Glyma.13G132700, Glyma.17G156100 and Glyma.13G133200 were selected as candidate genes for TSPL, whereas Glyma.13G174400, Glyma.13G174700, Glyma.16G012500, Glyma.17G156100, Glyma.19G161700 and Glyma.19G161800 were selected as candidate genes for TSPW. These results may be relevant for future attempts to modify soybean seed traits.

scholarly journals Fine Mapping of a Novel Major Quantitative Trait Locus, qPAA7, That Controls Panicle Apical Abortion in Rice

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaolei Wang ◽  
Lingfeng Li ◽  
Xiaotang Sun ◽  
Jie Xu ◽  
Linjuan Ouyang ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Gene Annotation ◽  
Functional Characterization ◽  
Recurrent Parent ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Trait Locus ◽  
Segment Substitution

The panicle apical abortion (PAA) causes severe yield losses in rice production, but details about its development and molecular basis remain elusive. Here, we detected PAA quantitative trait loci (QTLs) in three environments using a set of chromosome segment substitution lines (CSSLs) that was constructed with indica Changhui121 as the recurrent parent and japonica Koshihikari as the donor parent. First, we identified a novel major effector quantitative trait locus, qPAA7, and selected a severe PAA line, CSSL176, which had the highest PAA rate among CSSLs having Koshihikari segments at this locus. Next, an F2 population was constructed from a cross between CSS176 and CH121. Using F2 to make recombinantion analysis, qPAA7 was mapped to an 73.8-kb interval in chromosome 7. Among nine candidate genes within this interval, there isn’t any known genes affecting PAA. According to the gene annotation, gene expression profile and alignment of genomic DNA, LOC_Os07g41220 and LOC_Os07g41280 were predicted as putative candidate genes of qPAA7. Our study provides a foundation for cloning and functional characterization of the target gene from this locus.

scholarly journals Fine Mapping of A QTL Locus (QNFSP07-1) And Analysis of Candidate Genes For Four-Seeded Pods In Soybean

2021 ◽  
Author(s):  
Yingying Li ◽  
Chunyan Liu ◽  
Nannan Wang ◽  
Zhanguo Zhang ◽  
Lilong Hou ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Developmental Stages ◽  
Gene Annotation ◽  
High Ratio ◽  
Recurrent Parent ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Gene Map ◽  
Segment Substitution

Abstract The number of four-seeded pods is a quantitative trait in soybean [Glycine max (L.) Merr.] and is closely related to yield in terms of breeding. In this study, individuals with high ratio of four-seed pods which from chromosome segment substitution lines (CSSLs) that can be stably inherited were selected as the parent, and Suinong 14 (SN14) was used as recurrent parent to construct secondary mapping population via marker-assisted selection. The initial QTL mapping interval was 0.67 Mb and was located on Gm07. Based on the initial QTL mapping results, individuals that were heterozygous at the interval (36116118-37399738 bp) were screened, and the heterozygous individuals were subjected to inbreeding to obtain 13 F3 populations, with a target interval of 321 kb. Gene annotation was performed on the finely mapped interval, and 27 genes were obtained. Glyma.07G200900, Glyma.07G201200 were identified as candidate genes. qRT-PCR was used to measure the expression of the candidate genes at different developmental stages of soybean. The expression levels of the 2 candidate genes in terms of cell division (axillary buds, COTs, EMs) were higher than those in terms of cell expansion (MM, LM), and these genes play a positive regulatory role in the formation of four-seeded pods. Haplotype analysis shows that Glyma.07G201200 has two excellent haplotypes. Those results provide the information for gene map-based cloning and molecular marker assisted breeding of the number of four-seeded pod in soybean.

scholarly journals Combined Linkage Mapping and BSA to Identify QTL and Candidate Genes for Plant Height and the Number of Nodes on the Main Stem in Soybean

2019 ◽  
Vol 21 (1) ◽  
pp. 42 ◽  
Author(s):  
Ruichao Li ◽  
Hongwei Jiang ◽  
Zhanguo Zhang ◽  
Yuanyuan Zhao ◽  
Jianguo Xie ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Plant Height ◽  
Gene Annotation ◽  
Bulked Segregant Analysis ◽  
Main Stem ◽  
Nucleotide Polymorphisms ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Oil Crops ◽  
Trait Locus

Soybean is one of the most important food and oil crops in the world. Plant height (PH) and the number of nodes on the main stem (NNMS) are quantitative traits closely related to soybean yield. In this study, we used 208 chromosome segment substitution lines (CSSL) populations constructed using “SN14” and “ZYD00006” for quantitative trait locus (QTL) mapping of PH and NNMS. Combined with bulked segregant analysis (BSA) by extreme materials, 8 consistent QTLs were identified. According to the gene annotation of the QTL interval, a total of 335 genes were obtained. Five of which were associated with PH and NNMS, potentially representing candidate genes. RT-qPCR of these 5 candidate genes revealed two genes with differential relative expression levels in the stems of different materials. Haplotype analysis showed that different single nucleotide polymorphisms (SNPs) between the excellent haplotypes in Glyma.04G251900 and Glyma.16G156700 may be the cause of changes in these traits. These results provide the basis for research on candidate genes and marker-assisted selection (MAS) in soybean breeding.

scholarly journals Identification, pyramid and candidate genes of QTLs for associated traits based on a dense erect panicle rice CSSL-Z749 and five SSSLs, three DSSLs and one TSSL

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Dachuan Wang ◽  
Kai Zhou ◽  
Siqian Xiang ◽  
Qiuli Zhang ◽  
Ruxiang Li ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Candidate Genes ◽  
Complex Traits ◽  
Seed Set ◽  
Average Length ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Minor Qtls ◽  
Segment Substitution ◽  
Major Qtl

Abstract Background Seed-set density is an important agronomic trait in rice. However, its genetic mechanism is complex. Chromosome segment substitution lines (CSSLs) are ideal materials for studying complex traits. Results A rice CSSL, Z749, with a dense and erect panicle phenotype, was identified among progeny of the recipient parent Nipponbare and the donor parent Xihui 18. Z749 carried seven substitution segments (average length 2.12 Mb). Compared with Nipponbare, Z749 showed significant increases in the numbers of primary (NPB) and secondary branches (NSB), number of spikelets (SPP) and grains per panicle (GPP), seed-set density (SSD), and decrease in panicle length (PL). A secondary F2 population derived from a cross between Nipponbare and Z749 was used to map quantitative trait loci (QTLs) for associated traits. Fifteen QTLs distributed on chromosomes 5, 7, 8, and 10 were detected. The QTL qPL7 might be an allele of OsFAD8 and the remaining 14 QTLs (e.g., qSSD5 and qSSD10 etc.) might be novel. Fourteen QTLs were verified using five single-segment substitution lines (SSSLs). The seed-set density of Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). The QTLs qSSD10, qSSD5, and qSSD8 were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, and 8, respectively. Analysis of QTL additive effects indicated that qSSD5, qSSD8, and qSSD10 from Xihui18 increased seed-set density of Z749 by 14.10, 11.38, and 5.11 spikelets per 10 cm panicle, respectively. Analysis of QTL epistatic effects revealed that pyramiding of qSSD5 and qSSD8, qSSD5 and qSSD10, qSSD8 and qSSD10, and qSSD5, qSSD8 and qSSD10 produced novel genotypes with increased seed-set density. Conclusions Inheritance of seed-set density in Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). Then, they were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, 8, respectively. Two MAPK genes (OsMPK9 and OsMPK17) and one gene (candidate gene 6) involved in auxin metabolism might be candidate genes for qSSD5, and OsSAUR32 might be the candidate gene for qSSD8. Pyramiding of qSSD5, qSSD8, and qSSD10 enhanced seed-set density.

scholarly journals Identification, Pyramid and Candidate Genes of QTLs for Associated Traits Based on a Dense Erect Panicle Rice CSSL-Z749 and Five SSSLs, Three DSSLs and One TSSL

2021 ◽  
Author(s):  
Dachuan Wang ◽  
Kai Zhou ◽  
Siqian Xiang ◽  
Qiuli Zhang ◽  
Ruxiang Li ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Candidate Genes ◽  
Complex Traits ◽  
Seed Set ◽  
Average Length ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines ◽  
Minor Qtls ◽  
Segment Substitution ◽  
Major Qtl

Abstract Background Seed-set density is an important agronomic trait in rice. However, its genetic mechanism is complex. Chromosome segment substitution lines (CSSLs) are ideal materials for studying complex traits. Results A rice CSSL, Z749, with a dense and erect panicle phenotype, was identified among progeny of the recipient parent Nipponbare and the donor parent Xihui 18. Z749 carried seven substitution segments (average length 2.16 Mb). Compared with Nipponbare, Z749 showed significant increases in the numbers of primary (NPB) and secondary branches (NSB), number of spikelets (SPP) and grains per panicle (GPP), seed-set density (SSD), and decrease in panicle length (PL). A secondary F2 population derived from a cross between Nipponbare and Z749 was used to map quantitative trait loci (QTLs) for associated traits. Fifteen QTLs distributed on chromosomes 5, 7, 8, and 10 were detected. The QTL qPL7 might be an allele of OsFAD8 and the remaining 14 QTLs (e.g., qSSD5 and qSSD10 etc.) might be novel. Fourteen QTLs were verified using five single-segment substitution lines (SSSLs). The seed-set density of Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). The QTLs qSSD10, qSSD5, and qSSD8 were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, and 8, respectively. Analysis of QTL additive effects indicated that qSSD5, qSSD8, and qSSD10 from Xihui18 increased seed-set density of Z749 by 14.1, 11.38, and 5.11 spikelets per 10 cm panicle, respectively. Analysis of QTL epistatic effects revealed that pyramiding of qSSD5 and qSSD8, qSSD5 and qSSD10, qSSD8 and qSSD10, and qSSD5, qSSD8 and qSSD10 produced novel genotypes with increased seed-set density. Conclusions Inheritance of seed-set density in Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). Then, they were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, 8, respectively. Two MAPK genes (OsMPK9 and OsMPK17) and one gene (candidate gene 6) involved in auxin metabolism might be candidate genes for qSSD5, and OsSAUR32 might be the candidate gene for qSSD8. Pyramiding of qSSD5, qSSD8, and qSSD10 enhanced seed-set density.

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