Association mapping of loci controlling genetic and environmental interaction of soybean flowering time under various photo-thermal conditions

Abstract

BackgroundSoybean (Glycine max (L.) Merr.) is a short day plant. Its flowering and maturity time are controlled by genetic and environmental factors, as well the interaction between the two factors. Previous studies have shown that both genetic and environmental factors, mainly photoperiod and temperature, control flowering time of soybean. Additionally, these studies have reported gene × gene and gene × environment interactions on flowering time. However, the effects of quantitative trait loci (QTL) in response to photoperiod and temperature have not been well evaluated. The objectives of the current study were to identify the effects of loci associated with flowering time under different photo-thermal conditions and to understand the effects of interaction between loci and environment on soybean flowering.MethodsDifferent photoperiod and temperature combinations were obtained by adjusting sowing dates (spring sowing and summer sowing) or day-length (12 h, 16 h). Association mapping was performed on 91 soybean cultivars from different maturity groups (MG000-VIII) using 172 SSR markers and 5107 SNPs from the Illumina SoySNP6K iSelectBeadChip. The effects of the interaction between QTL and environments on flowering time were also analysed using the QTXNetwork.ResultsLarge-effect loci were detected on Gm 11, Gm 16 and Gm 20 as in previous reports. Most loci associated with flowering time are sensitive to photo-thermal conditions. Number of loci associated with flowering time was more under the long day (LD) than under the short day (SD) condition. The variation of flowering time among the soybean cultivars mostly resulted from the epistasis × environment and additive × environment interactions. Among the three candidate loci, i.e. Gm04_4497001 (near GmCOL3a), Gm16_30766209 (near GmFT2a and GmFT2b) and Gm19_47514601 (E3 or GmPhyA3), the Gm04_4497001 may be the key locus interacting with other loci for controlling soybean flowering time.ConclusionThe effects of loci associated with the flowering time of soybean were dependent upon the photo-thermal conditions. This study facilitates the understanding of the genetic mechanism of soybean flowering and molecular breeding for the improvement of soybean adaptability to specific and/or broad regions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3778-3) contains supplementary material, which is available to authorized users.

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

“…Another maturity locus, E7 , has been reported to control photoperiod sensitivity and is genetically linked to E1 and T ( Cober and Voldeng, 2001 ), which indicates that the QTL on chromosome 6 in this study might be E7 . In addition, there are other reported QTLs that overlap with the interval identified in this study ( Mansur et al, 1993 ; Orf et al, 1999 ; Funatsuki et al, 2005 ; Githiri et al, 2007 ; Liu and Abe, 2010 ; Oyoo et al, 2010 ; Sun et al, 2013 ; Hu et al, 2014 ; Zhang et al, 2015 ; Mao et al, 2017 ) (Supplementary Table 6 ). There may be several loci that affect multiple growth period-related traits such as time of first flowering, pod maturity, RP, and time to full maturity.…”

Determining the Relationship between Floral Initiation and Source–Sink Dynamics of Tomato Seedlings Affected by Changes in Shading and Nutrients

“…Leaves act as the source organ and photosynthesize, which is the main supply of starch and sucrose for plant growth and flower nutrition. Before the formation of flower bud, flower formation depends on carbohydrate reallocation from leaves (Lieth and Pasian, 1991;Mao et al, 2017;Nanda et al, 1995;Saito et al, 2015,). Therefore, the initiation of flower buds as the sink organ for biomass produced by leaves was delayed under shading treatments.…”

Crop genome‐wide association study: a harvest of biological relevance

“…This distinct genetic architecture provides a further opportunity to simultaneously manage trait mean and plasticity for a given environment or for a changing climate (Nicotra et al ., ). Flowering time is a classic example used in model and crop plants to study the genetic control of both mean and plastic phenotypes (Ungerer et al ., ; Anderson et al ., ; Brachi et al ., ; Mendez‐Vigo et al ., ; Mao et al ., ). Another recent study on sorghum flowering time (Li et al ., ) indicated that modeling plasticity can not only explain the genetic response to different environments, but also enable highly accurate prediction of trait performance in new environments.…”