| Direct-seeding cultivation is becoming one of the main trends in rice, because it can save both labour and water resource. The difference of sowing depth is significant, affecting the germination rate. However, the development of direct-seeding cultivation is restricted by seeding emergence. Mesocotyls elongation characterization promotes neat and fast emergence. Only a few germplasms mesocotyl length reaching to several centimeters has been reported. The semi-dwarf cultivated rice with shorter mescotyl and poor seeding emergence affects yield of rice. Therefore, the excavation in the rice germplasms with longer mesocotyl and higher germination rate should be a method with significant impact on the development of direct seeding rice.Mesocotyl length, an important agronomic traits is observed having positive correlation with the emergence of direct-seeding rice, however, the underlying genetic mechanism is unclear. Zhaxima and mowanggunei, the resources with longest mesocotyl having been selected by evaluating Mesocotyl lengths of 270 rice accessions composed by mini-core collection and drought resistance has been used to study the impact of light and temperature on it. Segregation analysis in F3 populations derived from a cross between two inbred lines, “zhaxima”(long mesocotyls) and “Hanhui No3”(short mesocotyls). Under 30℃ and dark germination conditions, the length of mesocotyl in F3 populations was measured, then whole genome resequencing and bulked segregant ananlysis(BSA) were used to identified genetic loci of the mesocotyl elongation. The main findings are as follows:(1)The experiment of the effect of temperature conditions on mesocotyl indicates that mesocotyls didn,t extend at low temperature, 15℃. As the temperature increasing, elongation of mesocotyl is fast. When the temperature reaches 30 ℃, the elongation of mesocotyl reached longest. However, higher temperature, 35℃and 40℃ inhibited mesocotyl elongation. The consistency of the result in both Zhaxima and mowanggunei was so high.(2) The experiment of the effect of light conditions on mesocotyl indicates that 3-5 days is mesocotyl quickly extended period. Mesocotyl elongation has been completed at the seventh days. With the light treatment 6 hours, the mesocotyl elongation was significantly inhibited implied that the halt of mesocotyl extended requires a certain amount of accumulated light.(3)The extreme plants of F2 derived from zhaxima and hanhui3 hao contain 1759 individuals. The mesocotyl data showed a normal distribution. Mesocotyl with elongation longer individual and hardly elongation individual was selected each 70, DNA was extracted to build long mesocotyls DNA pool and short mesocotyls DNA pool, sequenced with the Illumina HiSeqTM 2500. A total of 79 Gbp raw data was obtained, the sequence yieled 209375454 raw sequence for long mesocotyls DNA pool and 185547572 raw sequence for short mesocotyls DNA pool. 92.06% and 91.9% of sequence from long mesocotyl DNA pool and short mesocotyl DNA pool were mapped to the reference genome(RGAP7). The average Sequence depth of each individual was 60 ×, A total of 2384892 SNP and 359662 InDel were obtained. We also obtained 15 candidate regions, including 69 genes with non-synonymous SNP, 74 genes with synonymous SNP and 14 genes with frameshift SNP.(4)Genome-wide comparison of SNP between the long and short mesocotyl bulks constructed from F3 populations identified the mesocotyl elongation genetic loci. These sites are mainly located in chromosome 1、3、6、7、8、9、11、12. Analyed the difference of 23 genes between parents, a total of 11 genes was obtained as mesocotyl candidate genes. |
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