Fine mapping of a QTL locus (QNFSP07-1) and analysis of candidate genes for four-seeded pods in soybean

Yingying Li; Chunyan Liu; Nannan Wang; Zhanguo Zhang; Lilong Hou; Dawei Xin; Zhaoming Qi; Candong Li; Yan Yu; Hongwei Jiang; Qingshan Chen

doi:10.1007/s11032-021-01265-6

Fine mapping of a QTL locus (QNFSP07-1) and analysis of candidate genes for four-seeded pods in soybean

Mol Breed. 2021 Nov 20;41(11):71. doi: 10.1007/s11032-021-01265-6. eCollection 2021 Nov.

Authors

Yingying Li^#^{1

2}, Chunyan Liu^#¹, Nannan Wang^#³, Zhanguo Zhang¹, Lilong Hou¹, Dawei Xin¹, Zhaoming Qi¹, Candong Li³, Yan Yu⁴, Hongwei Jiang⁵, Qingshan Chen¹

Affiliations

¹ College of Agriculture, Northeast Agricultural University, Harbin, 150030 China.
² Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024 China.
³ HeiLongJiang Academy of Agricultural Sciences JiaMuSi Branch Institute, Jiamusi, 154000 China.
⁴ Changchun Sci-Tech University, Changchun, 130600 China.
⁵ Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, 130033 China.

^# Contributed equally.

Abstract

Soybean [Glycine max (L.) Merr.] is an important grain and oil crop in the world, and it is the main source of high-quality protein. The number of four-seeded pods is a quantitative trait in soybean and is closely related to yield in terms of breeding. Therefore, it is of great significance to study the inheritance of four-seed pods and to excavate related genes for improving soybean yield. 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. From 2006 to 2017, QTL analysis was performed using secondary mapping populations, and 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 (36,116,118-37,399,738 bp) were screened in 2018, 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 fine mapping interval, and 27 genes were obtained. Among 27 genes, Glyma.07G200900 and Glyma.07G201200 were identified as candidate genes. qRT-PCR was used to measure the expression of the 2 candidate genes at different developmental stages of soybean, and 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 of 2 candidate genes which shows that Glyma.07G201200 has two excellent haplotypes, and the significance level between the two excellent haplotypes at p < 0.05. Those results provide the information for gene map-based cloning and molecular marker-assisted breeding of the number of four-seeded pod in soybean.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-021-01265-6.

Keywords: Candidate genes; Fine mapping; Four-seeded pod; Haplotype analysis; QNFSP07-1; Soybean.