Position Mapping And Identification Of Soybean Locus J For Long Juvenile Trait

Soybean is a short day crop,and a model organism for photoperiodism research.It usually has low yield because precociously flowers and yields under short days with high temperatures.Long juvenility trait can make soybean has enough vegetative growth to ensure high yield under short days with high temperatures.Since its discovery and adoption,low-latitude regions became to be the main soybean production areas rapidly,which had been previously thought not to be suitable for soybean production.It significantly changing the situation of the world soybean production and trade.However,although the long juvenility trait was so important,but the underlying QTL/gene and the related genetic basis was unclear.Here,this research firstly analyzed the juvenility of soybeans sowed at different sites with different latitudes and the juvenility of soybeans sowed on different dates at low-latitude,then filtered out the conventional-juvenile and long-juvenile soybeans.Secondly,it mapped the physical position of the long-juvenile QTL J by RAD-Seq and linkage analysis of the RIL population by crossing Zhonghuang 24(conventional-juvenile soybean)and Huaxia 3(long-juvenile),and identified the J gene by refining the polymorphism information in the region of QTL J after whole-genome resequencing the RIL parents.Thirdly,it cloned the J gene and identified its molecular functions by the transgenic over-expression analysis in Arabidopsis and the transgenic compensation analysis in the long-juvenile Huaxia 3.Finally,it performed the haplotype analysis of the J gene in 171 varieties from different countries.More are detailed as following:1.By analyzing the juvenility trait of soybeans from different latitudes,the results showed that the juvenility trait is major determined by the inner genetic mechanism and also regulated by outer environments.The long-juvenile soybeans were also defined,that is,Baxi 3,Baxi 8,Baxi 13,Baxi 16,Baxi 17,Guixiadou 2,Huaxia 3,Sudan 2,Sudan 3 and Sudan 4.Of them,Huaxia 3 showed a consistent long juvenility.2.By analyzing the juvenility trait of Zhonghuang 24 × Huaxia 3 RIL population sowed in Guangzhou,the results showed that the juvenility trait exhibited a bimodal distribution not only in F2 population but also in high-generation populations and F2 population had a higher ratio of short juvenility,suggesting that the juvenility trait is controlled by a recessive allele of J.Other genes also might function there secondary.3.By comparing the juvenility of Zhonghuang 24 × Huaxia 3 RIL population sowed in Guangzhou and in Beijing,the results showed that the juvenility trait is affected by both sowing date and latitude with multiple genes involved.However,the major-effect gene might differ in different environments.In Guangzhou with flowering-inducing short days and high temperatures,the juvenility trait is major controlled by long-juvenile gene J,while in Beijing with flowering-inhibiting long days,it is major controlled by photoperiod-related genes.4.By RAD-Seq analysis of Zhonghuang 24 × Huaxia 3 RIL population,high-quality polymorphism sites were gotten.Moreover,the population had the allele frequency close to the ideal ratio of 1:1 and exhibited a balanced state without any obvious genetical structure,suggesting that it is very suitable for QTL mapping.Genetic mapping and linkage analysis mapped the QTL J into a 900 kb region of Chr04_bin13-13-13(Chr04:4036172-4909316).5.By the whole-genome resequencing of the parents of Zhonghuang 24 and Huaxia 3,the polymorphism information was refined in the region of QTL J,and the J gene was targeted as Glyma.04G050200,which is the only one gene in the QTL J harboring a single-nucleotide frameshift deletion and also a homolog gene of Arabidopsis circadian clock gene ELF3.6.By sequencing analysis of the J gene,the results showed that the J allele in the conventional-juvenile Zhonghuang 24 encodes a protein with 714 amino acids,while the j allele in the long-juvenile Huaxia 3 encodes a prematured function-lost protein with only 443 amino acids due to a single-nucleotide frameshift deletion.Moreover,the indel polymorphism cosegregated with the long juvenility trait in Zhonghuang 24 × Huaxia 3 RIL population.Thus it suggested that the frameshift indel mutation of the J gene might be the molecular basis of the long juvenility trait.7.By identifying the molecular function of the J gene,the results showed that the J gene is mainly expressed in vegetative tissues and its over-expression not only promoted flowering in Arabidopsis,but also compensated the j allele to shorten the juvenility.Thus,it demonstrated at the molecular level that J is the long-juvenility gene and its mutation is the molecular basis of the long juvenility trait.8.By haplotype analysis of the J gene with different soybean sources,the results showed that J has evolved in at least four haplotypes HT1,HT2,HT3 and HT1 m to adapt to different environments.Moreover,J is related with the geographical adaption of soybean.My research paved a way to further elucidate the genetic mechanism of the long juvenility trait,take advantage of the elite germplasm from middle and high latitudes to breed soybean varieties adapted to low-latitude topical and subtropical regions,and even directionally design the soybean maturity to breed soybeans with high yield and good quality.