Study On Genetic Basis Of Backbone Parents In Early Conventional Rice

As one of the main ecological types of rice in China,double season-cropping early indica rice is widely cultivated in south China and the middle and lower reaches of the Yangtze river basin.Early conventional rice not only plays an important role in rice production,but also is the main source of early hybrid rice varieties'restorer lines and sterile lines.The early conventional rice breeding has made great progress in the middle and lower reaches of the Yangtze river basin since the"dwarf breeding".The yield per hectare has increased from less than 4.5t to more than 6t,or even exceed 6.75 t/hm² in some areas with the development and commercial application of some super-rice varieties such as Zhongzao 22,Zhongjiazao17 and Zhongzao 35.But after 2000,especially around 2009,few new varieties could registered since ZZ35 and ZZ39 were used as the control of national and regional level adaption test due to the lower performance.Breeders find they facing some challenges that cross lines are usually derived from a few backbone parents,difficulty in early generations selection because of the similar parents and little traits segregation in separate generations;High similarity between new-bred varieties and their parents;The new registered varieties were derived from a few backbone parents;Selection in different locations and seasons were just depended on experience but not systematic scientific selection indexes.These issues have effected the efficiency of conventional breeding.The present study explored the genetic genealogy relationship and analyzed the genetic diversity with the main conventional double season rice varieties in the middle and lower reaches of the Yangtze river basin.In order to illuminate the repeatability of traditional experience breeding,the specificity of the new lines derived from Zhongzao 35 and Zhongzao 39 were detected with the molecular markers.Meanwhile,high-throughput sequencing was used to analyze the genetic mechanism of backbone parent Jiayu 253.In addition,to explore the major indexes in the different seasons of conventional early rice,the main agronomic traits for different seasons and locations were investigated with planted varieties developed after 2000.The main results were summarized as following:1?Sixty two early conventional rice varieties registered at or above the provincial level after 2000in the Yangtze River Basin were analyzed using 50 pairs of SSR primers with high polymorphism,good stability,and even distribution on 12 chromosomes of rice to construct SSR fingerprints of conventional early rice.Cluster analysis was conducted with NTSYS PC Version 2.10e software and UPGMA cluster analysis method.A total of 154 polymorphic bands were detected among 62 rice lines,2 to 6 alleles were detected for each marker with an average of 3.08.Primers polymorphism information content?PIC?value ranged from 0.03 to 0.75,with an average of 0.36.Cluster analysis with NTSYS PC Version 2.10e software showed that the genetic similarities ranged from 0.66 to 1.00.The 62 varieties could be divided into two major types as varieties in Zhejiang Province and varieties outside the province at the similarity coefficient of 0.73 with small difference between groups.Combination with the pedigree relationship,it was revealed that the genetic background of early rice varieties in this study was relatively narrow.2?Two high yielding varieties,Zhongzao 35 and Zhongzao 39,were used as the main parents to cross with other varieties?parents?in breeding program.Genetic Stable lines were obtained after consecutive six seasons selection according to conventional cross breeding method.Some stable lines were hardly distinguished with Zhongzao 35 or Zhongzao 39 on the phenotype,These stable lines were detected by SSR molecular markers in the succession two years to develop new lines according to the demands of DUS.96 pairs of SSR primers were used to detect the similar lines in F₇ generation.The results showed that 2 of 23 and 7 of 44 combinations,11 of 77 and 25 of 166 lines could not be detected any difference with Zhongzao 35 and Zhongzao 39,counted for 8.7-15.9%and 14.3-15.1%in two years,respectively.The results indicated that the process of breeding can be repeated in a certain extent because of the consistency of the selection indexes and preference.3?To study the genetic mechanism of backbone parents in early conventional rice,conventional rice backbone parent Jiayu 253 were used to de novo sequencing,24 rice materials?including 10 lineal directly derivatives of Jiayu 253,Zhongxuan 181 and its 6 lineal derivatives and 9 contemporary high yielding varieties?and an ancestor variety IR8 were used to re-sequencing.A total of 75.8Gb?69.3Gb clean data?of high quality genomic sequence were generated for Jiayu 253,representing 188.1-fold coverage of the entire rice genome.De novo assembly of the Illumina reads resulted in a final assembly of 383.9 Mb.Genome annotated showed that,40031 gene were derived,approximately 98.07%of the predicted genes had either known homologs or could be functionally classified.The gene family analysis showed that there were 32 gene families specificly existence in Jiayu 253.The total re-sequencing data of 25 samples were 382.2Gbp,and 1678566 original SNPs were detected in the whole population.The phylogenetic tree results were roughly matched but not idential with cluster analysis results based on pedigree and molecular markers.LD analysis revealed that the linkage degree of the three populations was higher than normal rice populations,probably due to the strong artificial selection in the breeding process.A total of 676 idential fragments unevenly distributed on the chromosomes were detected in the population of Jiayu 253 and its 10 derivatives.The biological function of the specific gene families of the backbone parents is still under further analysis.4?Twenty four early conventional rice varieties were cultivated in Hangzhou?summer-normal planting season,autumn-abnormal planting season?and Hainan?winter-abnormal planting season?respectively.Plant height,seed setting rate,1000 grain weight,flag leaf length,width,ratio,effective panicle number and other major agronomic traits in different locations and seasons were investigated to summarize the characteristics of different seasons,places and to provide theoretical basis and reference for establishing different season selection indexes.In summer season of Hangzhou,varieties with good yield traits should be selected.In autumn season of Hangzhou,less attention should be paid for the long flag leaf.In Hainan season,more attention should be paid for the uniformity of heading and less attention for the plant height.Other traits can be determined according to the specific growth environment and the breeding objectives of breeders.