Quantitative Trait Locus Mapping of Flowering Time and Maturity in Soybean Using Next-Generation Sequencing-Based Analysis

Abstract

Soybean (Glycine max L.) is a major legume crop that is mainly distributed in temperate regions. The adaptability of soybean to grow at relatively high latitudes is attributed to natural variations in major genes and quantitative trait loci (QTLs) that control flowering time and maturity. Identification of new QTLs and map-based cloning of candidate genes are the fundamental approaches in elucidating the mechanism underlying soybean flowering and adaptation. To identify novel QTLs/genes, we developed two F8:10 recombinant inbred lines (RILs) and evaluated the traits of time to flowering (R1), maturity (R8), and reproductive period (RP) in the field. To rapidly and efficiently identify QTLs that control these traits, next-generation sequencing (NGS)-based QTL analysis was performed. This study demonstrates that only one major QTL on chromosome 4 simultaneously controls R1, R8, and RP traits in the Dongnong 50 × Williams 82 (DW) RIL population. Furthermore, three QTLs were mapped to chromosomes 6, 11, and 16 in the Suinong 14 × Enrei (SE) RIL population. Two major pleiotropic QTLs on chromosomes 4 and 6 were shown to affect flowering time, maturity, and RP. A QTL influencing RP was identified on chromosome 11, and QTL on chromosome 16 was associated with time to flowering responses. All these QTLs contributed to soybean maturation. The QTLs identified in this study may be utilized in fine mapping and map-based cloning of candidate genes to elucidate the mechanisms underlying flowering and soybean adaptation to different latitudes and to breed novel soybean cultivars with optimal yield-related traits.

Keywords: flowering time; maturity; quantitative trait loci; reproduction period; soybean.

FIGURE 1

Phenotypes of the parents of SE population. (A–D) Plants when Suinong 14 had flowered, while Enrei was still in the vegetative growth stage. (A,C Suinong 14; B,D Enrei). (E). Plants when Suinong 14 has already fully matured, while Enrei was still in the seed filling growth stage. Left is Suinong 14 and right is Enrei. (F–H) Phenotypes data of the parents in 2016, Harbin. (I–K) Phenotypes data of the parents in 2017, Harbin. DAE, day after emergence.

FIGURE 2

Phenotypes of the parents of DW population. (A–D) Plants when Dongnong 50 had flowered, while Williams 82 was still in the vegetative growth stage. (A,C Dongnong 50; B,D Williams 82). (E) Plants when Dongnong 50 has already fully matured, while Williams 82 was still in the seed filling growth stage. Left is Dongnong 50 and right is Williams 82. (F–H) Phenotypes data of the parents in 2016 Harbin. (I–K) Phenotypes of the Parents in 2017, Harbin. DAE, day after emergence.

FIGURE 3

The genetic map of RIL populations. (A,B) Genetic map of SE and DW RIL population constructed with HighMap software, respectively. Chr., chromosome.

FIGURE 4

The LOD value of the QTLs detected in SE RIL population under different environments and QTLs detected using the average data of different environments (MQM method). (A) QTLs of Flowering time trait (R1). (B) QTLs of maturity time trait (R8). (C) QTLs of reproductive period trait (RP). Harbin, 2016: The data of year 2016 in Harbin. Mudanjiang, 2016: The data of year 2016 in Mudanjiang. Harbin, 2017: The data of year 2017 in Harbin. Average: the average data in different environments. Chr., chromosome.

FIGURE 5

The LOD value of the QTLs detected in DW RIL population under different environments and QTLs detected using the average data of different environments (MQM method). (A) QTLs of Flowering time trait (R1). (B) QTLs of maturity time trait (R8). (C) QTLs of reproductive period trait (RP). Harbin, 2016: The data of year 2016 in Harbin. Mudanjiang, 2016: The data of year 2016 in Mudanjiang. Harbin, 2017: The data of year 2017 in Harbin. Average: the average data in different environments. Chr., chromosome.

FIGURE 6

The high confidence interval of QTL detected on chromosome 4 (CIM method). The red rectangle represents the high confidence interval between markers Gm_69 and Gm_80 with physical positions from 13,212,370 to 43,843,500.

FIGURE 7

The high confidence interval of QTL detected on chromosome 6 (CIM method). Within the genetic interval from 77.66 cM to 87.4 cM between markers Marker381872 and 386215 with physical positions 15,741,239–28,154,637, no recombination was found according to the sequencing result. The red rectangle represents the high confidence interval between markers Marker386215 and 395918 with physical positions from 28,154,637 to 42,126,497.

FIGURE 8

Annotation information of genes in the high confidence interval of QTL detected on chromosome 4 through Gene ontology (GO) analysis.

FIGURE 9

Annotation information of genes in the high confidence interval of QTL detected on chromosome 6 through Gene ontology (GO) analysis.

FIGURE 10

Nucleotide sequence polymorphism of parents of the two RIL populations within the intervals of two major QTLs. (A) Polymorphism SNP number between parents Dongnong 50 and Williams 82 within QTL interval from 9,226,038 to 44,284,689 on chromosome 4. (B) Polymorphism SNPs and Indels between Suinong 14 and Enrei within the QTL interval from 14,777,428 to 47,231,089 on chromosome 6. (C) Polymorphism SNPs and Indels leading to amino acids (AA) change in the 1.5-LOD drop QTL interval from 13,212,370 to 43,843,500 on chromosome 4 between Dongnong 50 and Williams 82. Total: all SNPs and Indels; SE/DW: the same polymorphism SNPs and Indels between four parents of the two RIL populations which were with the same variation position and variation type; DW: SNPs and Indels uniquely detected between Dongnong 50 and Williams 82. (D) Polymorphism SNPs and Indels within gene (5′UTR, CDS, 3′UTR) in the 1.5-LOD drop QTL interval from 15,741,239 to 42,126,497 of chromosome 6 between parents Suinong 14 and Enrei. Total: all SNPs and Indels; Within CDS: SNPs and Indels number within the CDS region of one gene; Synonymous: variations that resulted in no change in amino acids.