Genetic analyses for deciphering the status and role of photoperiodic and maturity genes in major Indian soybean cultivars

Abstract

Allelic combinations of major photoperiodic (E1, E3, E4) and maturity (E2) genes have extended the adaptation of quantitative photoperiod sensitive soybean crop from its origin (China ∼35◦N latitude) to both north (up to ∼50◦N) and south (up to 40◦S) latitudes, but their allelic status and role in India (6-35◦N) are unknown. Loss of function and hypoactive alleles of these genes are known to confer photoinsensitivity to long days and early maturity. Early maturity has helped to adapt soybean to short growing season of India. We had earlier found that all the Indian cultivars are sensitive to incandescent long day (ILD) and could identify six insensitive accessions through screening 2071 accessions under ILD. Available models for ILD insensitivity suggested that identified insensitive genotypes should be either e3/e4 or e1 (e1-nl or e1-fs) with either e3 or e4. We found that one of the insensitive accessions (EC 390977) was of e3/e4 genotype and hybridized it with four ILD sensitive cultivars JS 335, JS 95-60, JS 93-05, NRC 37 and an accession EC 538828. Inheritance studies and marker-based cosegregation analyses confirmed the segregation of E3 and E4 genes and identified JS 93-05 and NRC 37 as E3E3E4E4 and EC 538828 as e3e3E4E4. Further, genotyping through sequencing, derived cleaved amplified polymorphic sequences (dCAPS) and cleaved amplified polymorphic sequences (CAPS) markers identified JS 95-60 with hypoactive e1-as and JS 335 with loss of function e3-fs alleles. Presence of photoperiodic recessive alleles in these two most popular Indian cultivars suggested for their role in conferring early flowering and maturity. This observation could be confirmed in F2 population derived from the cross JS 95-60 × EC 390977, where individuals with e1-as e1-as and e4e4 genotypes could flower 7 and 2.4 days earlier, respectively. Possibility of identification of new alleles ormechanism for ILD insensitivity and use of photoinsensitivity in Indian conditions have been discussed.

Positional Cloning of the Flowering Time QTL qFT12-1 Reveals the Link Between the Clock Related PRR Homolog With Photoperiodic Response in Soybeans

“…Various allelic combinations at the E1 , E2 , E3 , and E4 loci controlling the absence of or reduced photoperiod sensitivity determine the diversification of soybean maturity and adaptation at different latitudes (Xu et al, 2013; Tsubokura et al, 2013a; Tsubokura et al, 2013b; Zhai et al, 2014; Jiang et al, 2014; Kurasch et al, 2017; Langewisch et al, 2017; Li et al, 2017; Gupta et al, 2017). These genes or loci also influence the yield, adaptability, and quality of soybeans (Xia et al, 2012b; Sayama et al, 2010; Guo et al, 2015).…”

Environmental and Genetic Regulation of Plant Height in Soybean

“…In order to facilitate the development of such breeding programs, various ecological environments have been classi ed and characterized throughout the main soybean producing countries [74][75][76][77][78]. For example, photoperiod and temperature are critical environmental factors that in uence soybean shoot architecture development [38][39][40][79][80][81][82]. In soybean, the effect of photoperiod on a variety of developmental processes has been well described, and more than 10 genetic loci sensitive to photoperiod changes have been cloned [40-42, 44, 83].…”

“…However, optimal temperatures vary among different physiological processes, with, for example, 18°C being reported as the optimal night temperature for tomato stem elongation [37]. As a facultative short-day plant, soybean is in uenced by both day-length and temperature, both of which also play critical roles in the formation of shoot architecture [38][39][40]. For example, soybean exposed to short photoperiods and high temperatures in low latitude regions typically exhibit early owering, short periods of vegetative growth, short plant heights, and great reductions in yield [41,42].…”

QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding

“…The maturity genes B3 DNA binding protein gene ( E1 ), GIGANTEA ( E2 ), GmPhyA3 ( E3 ), and GmPhyA2 ( E4 ) down regulate expression of GmFT2a ( E9 ) and GmFT5a to delay flowering and maturation under the long day condition, suggesting that GmFT2a and GmFT5a are the major targets in the control of flowering in soybean (Kong et al, 2010; Thakare et al, 2011; Watanabe et al, 2011; Xia et al, 2012; Zhao et al, 2016). The genes and alleles identified for flowering and maturity traits in soybean have been validated in several studies using germplasm from many countries (Tsubokura et al, 2013, 2014; Jiang et al, 2014; Langewisch et al, 2014; Zhai et al, 2014; Gupta et al, 2016). A lot of information has been generated on flowering and maturity genes in soybean which also reveals the presence of legume specific unique genes in soybean i.e., B3 DNA binding protein gene of E1 loci.…”