QTL Mapping Of Characters Related To Seed Reserve Utilization During Seed Germination In Rice (Oryza Sativa L.)

Seed reserve utilization is an important character during seed germination. In this study, one population of recombinant inbred lines (RILs) derived from a cross between the japonica rice variety Jiucaiqing and indica IR26 were used to determine the genetic characteristics of seed reserve utilization during the early (day 6), middle (day 10) and late (day 14) germination stages. The results showed that the seedling dry weight (SDW) and weight of the mobilized seed reserve (WMSR) were increased, while the seed reserve utilization efficiency (SRUE) decreased, during the process of seed germination. There were significant differences for seed reserve utilization among the parents and RILs. Correlation analysis indicated that the SDW and WMSR are affected by the seed dry weight, while not the SRUE. A total of 21 unconditional additive quantitative trait loci (QTL),21 conditional additive QTLs and eight epistatic QTLs were identified at three germination stages. Among them, twelve additive and three epistatic QTLs for SDW, eight additive and three epistatic QTLs for WMSR and thirteen additive and two epistatic QTLs for SRUE were identified, respectively. The phenotypic variation explained by each additive QTL, epistatic QTL and QTL X development interaction ranged from 6.10 to 23.91%,1.79 to 6.88% and 0.22 to 2.86%, respectively. Two major additive QTLs qWMSR7.1 and qSRUE4.3 were identified, and each QTL could explain more than 20% of the total phenotypic variance. By comparing the chromosomal positions of these additive QTLs with those previously identified,36 QTLs were found to map near the additive QTL identified in this study while eleven QTLs might represent novel genes. The best four cross combinations of each trait for the development of RIL populations were selected. The selected RILs and the identified QTLs might be applicable to improve rice seed reserve utilization by the marker-assisted selection (MAS) approach.In this study, the japonica rice variety Jiucaiqing and the indica variety IR26 and their population of recombinant inbred lines (RILs) were used to determine the dynamics of seed reserve utilization, storage carbohydrate mobilization and hydrolytic gene expression and their relationships during seed germination. Three traits for seed reserve utilization including seedling dry weight (SDW), the weight of mobilized seed reserve (WMSR) and the seed reserve utilization efficiency (SRUE), three traits for storage carbohydrate mobilization including the sucrose (SC), glucose (GC) and fructose (FC) and four traits for hydrolytic gene expression including amylases (AMY) and sucrose synthase (SUS) activities and a-amylase and sucrose synthase genes were investigated. The SDW, WMSR, SRUE, FC, AMY and SUS were increased with the process of seed germination, while the SC and GC were limit dropped after the first rise slightly. The seed reserve depletion starts after initial imbibition and a rapid breakdown of seed reserve in endosperm starts after about 4 days of germination. The FC was found to constitute the greatest portion of the soluble sugars throughout the germination stage. Correlation analysis showed that there are significant positive relationships between the SC, GC, FC, AMY and SUS with the SDW, WMSR and SRUE respectively. There was genetic difference in these traits between the Jiucaiqing and IR26. Jiucaiqing had the higher WMSR while IR26 had the higher SRUE, AMY and SUS. A total of twelve QTLs for SC, AMY and SUS activities were mapped on chromosomes 1,4,5,6,7,9 and 11, respectively. The amount of variation explained by an individual QTL ranged from 5.27% to 26.45%. Among them, two QTLs (qSCl and qSUS7.2) with R2>20% were detected. By comparing the chromosomal positions of these QTLs with those previously identified, three QTLs might represent novel genes. Seven α-amylase genes (OsAmylA, OsAmy2A, OsAmy3A, OsAmy3B, OsAmy3C,OsAmy3D and OsAmy3E) and six sucrose synthase genes (OsSusl, OsSus2, OsSus3, OsSus4, OsSus5 and OsSus6) were analyzed in rice embryo at the early germination stages, which indicated that the OsAmy2A and OsSus5 and OsSus6 might play important roles in seed reverse utilization. The identified QTLs and genes might be applicable to improve rice seed reserve utilization by the marker-assisted selection (MAS) approach.In this study,276 indica rice varieties obtained from 18 global regions of the world were used to carry out association mapping for three traits of seed reserve utilization, including seedling dry weight (SDW), weight of mobilized seed reserve (WMSR) and seed reserve utilization efficiency (SRUE), at the early (Day 10) and late (Day 20) germination stages. Genome-wide association mapping using information from 159 simple sequence repeat (SSR) markers and using general linear model (Q, GLM) and mixed linear model (Q+K, MLM) were performed to identify the marker loci/QTLs underlying the naturally occurring variations of seed reserve utilization in rice. The genotyping demonstrated that the average polymorphic information content (PIC) value of varieties is 0.4262 and these varieties could be divided into two main cluster groups. There were significant variety differences in seed reserve utilization among the indica rice collections. The GLM detected 81 marker-trait associations involving 46 SSR markers for three traits, while 83 marker-trait associations involving 48 SSR markers identified by MLM. Of them, a total of 67 QTLs for three traits involving 41 SSR markers were detected by both GLM and MLM methods, including 18,22 and 27 QTLs for SDW, WMSR and SRUE, respectively. The identification of co-localized QTL occurred in 17 markers regions, among them 3 for SDW and WMSR,5 for WMSR and SRUE, and 9 for SDW, WMSR and SRUE. More QTL for SDW and WMSR were detected at the early stage, while more QTLs for SURE identified at late stage. Twelve QTL were co-localized among the two germination stages, of them,3 for SDW,8 for WMSR and 1 for SRUE. By comparing the chromosomal positions of these QTLs with those previously identified,51 QTLs might represent novel genes. According to the estimates for the allelic effects of the detected QTLs, the best three cross combinations of each trait for the development of RIL populations were selected; e.g., the cross of Alo-Combo and Ruiyu406-23 improve seedling dry weight and the combination of cultivars Mengwanggu, Alo-Combo and Honglaosuya might pyramid 67 elite alleles. The selected varieties and the identified QTLs might be applicable to improve rice seed reserve utilization by the marker-assisted selection approach.