Identification of alleles related to rice traits using association analysis and haplotyping under normal and drought stress

Background Rice after wheat is the most important and essential foodstuff in the world and accounts for 40 to 50 percent of the world's food. Rice per capita consumption in iran is 40 kg. Rice consumption in Iran has increased since the 50 and is considered as an essential commodity and the second most important nutrient after wheat. Drought stress is a kind of potential reduction of soil water and in such a situation, plant to maintain and continue water absorption can regulate osmotic potential. The concept of stress in the plant is the negative and severe effect of a number of living or non-living factors in the plant. The environment is on the plant's natural plant that can disrupt dry matter production and decrease its yield. Plant adaptation behavior to drought stress plays an important role in stress tolerance. These behaviors are controlled and controlled by the genes and can function under non-stress conditions. The purpose of this experiment was to investigate the allelic variation, coupling analysis and haplotypes of continuous microsatellite markers to drought tolerance genes in rice. Materials and methods The plant material studied in this research, which included 48 varieties of rice, was prepared from Rice Research Center of iran, (IRRI) research institute and lines produced at Gonbad-e-Kavos University. In a completely randomized block design with Three replicates in two separate floodwaters (without stress) and drought stress in terms of diversity of morphological and genetic traits in Babol province in 2016 were surveyed. Irrigation was done from 40 days after transplantation, which was carried out on 2 irrigation regimes based on the crop year. In the processing stage, grain yield was taken from a surface area of one square meter and grain yield was calculated with a moisture content of 14%. Other traits including 100 grains weight, number of stems, number of filled grains, number of pods, plant height, panicle length, number of panicles, stem diameter, grain length, grain width, grain shape, straw weight, length of period, Flag leaf length, flag leaf width of 10 plants were randomly selected and traits were measured. Molecular studies were performed with nine microsatellite markers related to drought stress tolerance. Findings Considering the significance of interactions between cultivars and cultivations, the variance of the compound was divided into two distinct normal and stresses (Table 1-4, 2-4, and 3-4). Analysis of variance showed both in normal conditions and in drought stress Genotypes were significantly different for all studied traits in both conditions. The 48 genotypes examined were based on 9 microsatellite markers in a total of 31 alleles with an average of 44.3 alleles per gene site. The RM60 marker had the highest number of alleles (six), and RM 324 and RM472 markers had the lowest allele count (two). The average content of multiform data log (PIC) was 51.1, which showed RM22 and RM12093 with 0.68 and RM324 with the lowest of 0.14 (PIC). The results of coupling analysis showed that in the traits of yield and yield components for number of clusters, the number of three negative alleles (RM12093-A, RM60-B, RM22-E) and four alleles (RM216-B, RM28166-B, RM28166- C and RM324-A) had positive regression coefficients. For the number of grains in the cluster, there was a positive allele (RM22C) allele. Three positive alleles (RM19367-A, RM216-A and RM22-D) and a negative allele (RM472-A) were also detected for 1000-grain weight. The functional attribute was correlated with only one allele (RM510-C). The haplotype evaluation divided the microsatellite markers of the genotypes into 25 haplotype groups, of which 23 haplotypes were isolated and the other two groups had two genotypes in their subset. haplotype 1 group (48 and 47 genotypes) had the highest yield of 5540.9 kg / ha and in some cases it could be said that it had the highest drought tolerance. Discussion The comparison of the results of haplotype analysis and the analysis of the association of alleles with the evaluated traits showed that there is a correlation between the results of these two methods of examining the data for the obtained data. Combined analysis of variance showed that most of the studied traits were significant at 1% probability level.