Functional Nucleotide Polymorphisms Of Abiotic Stress Resistance Genes In African Rice And Asian Rice

Rice is the staple food for more than half of the world's humans.However,rice is domesticated under relatively good environmental conditions and is sensitive to most abiotic stresses.Therefore,complex and changeable abiotic stresses are one of the main factors limiting rice growth,development,biological yield and quality.In this study,A total of 48 rice materials from 6 types.5 African rice,4 NERICA rice,12 introgression lines,16 Indica rice,8 japonica rice and 3 weedy rice were selected.By cloning and sequencing four abiotic stress resistance gene sequences,the DNA sequences and polymorphisms of four abiotic stress resistance genes were explored,and the variation of abiotic stress resistance related genes in different rice germplasms was discovered.Combining with the related phenotypic traits data,the rice germplasm materials containing favorable alleles were screened.In order to provide excellent germplasm resources and theoretical basis for the breeding of stress-resistant rice varieties.The results of this study are as follows:1.Two haplotypes and three variant loci were identified in the transcriptional region(coding region + UTR region)of salt tolerance gene ZFP179 of 48 rice varieties.The genetic distance between haplotypes was 2.341.Haploid ZFP179.Hap1 was divided into group ST I and haplotype ZFP179.Hap2 into group ST II.There are two coding sequences in the two haplotypes,and the translated amino acid sequences are also different.There are two mutation sites of amino acid sequences in the two haplotypes.In further codon preference analysis of ZFP179 gene,it was found that the salt tolerant gene ZFP179 allele preferred codon ending with base G/C.2.Six haplotypes and ten mutation loci were identified in the transcriptional region(coding region + Intron region + UTR region)of drought-tolerant gene OsRCI2-5 of 48 rice varieties.The average genetic distance between the six haplotypes was 1.053,the maximum genetic distance was 1.265 and the minimum genetic distance was 0.894.Haplotypes OsRCI2-5.Hap1 were grouped into DT1 I,haplotypes OsRCI2-5.Hap3,OsRCI2-5.Hap4,OsRCI2-5.Hap5 and OsRCI2-5.Hap6 were grouped into DT1 II,haplotypes OsRCI2-5.Hap2 were grouped into DT1 III.There are three coding sequences in six haplotypes,but the amino acid sequences obtained by translation are the same.In further codon preference analysis of OsRCI2-5 gene,it was found that the drought-tolerant gene OsRCI2-5 allele preferred codon ending with base G/C.3.Seven haplotypes and twenty-nine mutation sites were identified in the transcriptional region(coding region + UTR region)of drought-tolerant gene OsDT11 of 48 rice varieties.The average genetic distance between the seven haplotypes was 1.472,the maximum genetic distance was 2.446 and the minimum genetic distance was 0.087.Haploid OsDT11.Hap3 was divided into group DT2 I,haplotype OsDT11.Hap4,OsDT11.Hap5,OsDT11.Hap6 and OsDT11.Hap7 were divided into group DT2 II,haplotype OsDT11.Hap1 and OsDT11.Hap2 were divided into group DT2 III.There are three coding sequences in seven haplotypes,and two amino acid sequences can be obtained by translation.In further codon preference analysis of OsDT11 gene,it was found that the drought tolerant gene OsDT11 allele had no obvious preference for codon 3 base.4.Seven haplotypes and twelve mutation loci were identified in the transcriptional region(coding region + UTR region)of the cold-tolerant gene qLTG3-1 of 48 rice varieties.The average genetic distance between the seven haplotypes was 1.488,the maximum genetic distance was 2.472 and the minimum genetic distance was 0.234.Haplotypes qLTG3-1.Hap1,qLTG3-1.Hap2,qLTG3-1.Hap3 and qLTG3-1.Hap7 were grouped into LTR I,haplotypes qLTG3-1.Hap5 were grouped into LTR II,haplotypes qLTG3-1.Hap4 and qLTG3-1.Hap6 were grouped into LTR III.Seven coding sequences exist in seven haplotypes,which can be translated into seven amino acid sequences.In further codon preference analysis of qLTG3-1 gene,it was found that haplotypes of drought-tolerant gene qLTG3-1 preferred codons ending with base G/C.5.In the analysis of Selection pressure,we found that salt-tolerant gene ZFP179 was strongly influenced by positive selection effect,drought-tolerant gene OsRCI2-5 was strongly influenced by purify selection effect drought-tolerant gene OsDT11 might be inclined to neutral evolution,and cold-tolerant gene qLTG3-1 was influenced by purify selection effect.6.The results were obtained by Multiple comparisons with phenotypic traits.There were significant differences in relative root length between two ZFP179 haplotypes under salt stress.Under drought stress,5 OsRCI2-5 haplotypes had significant differences in 11 agronomic traits such as survival rate,relative stem length and relative root number,and 6 OsDT11 haplotypes had significant differences in 13 agronomic traits such as survival rate,relative stem length and relative root number.Under cold stress,the average germination days and relative germination days of five qLTG3-1 haplotypes were significantly different.