Genetic Analysis Of The Evolution Of Major Inbred Rice Cultivars In China

Rice（Oryza sativa L.）is one of the most important food crops in the world.Inbred rice and hybrid rice are two types of rice cultivars in Chinese rice production,and their planting proportions are close recently.Since the 1950s,about 3,000 rice cultivars with an annual planting area of more than 6,667 hectares（100,000 mu）have been bred in China,of which about 80%are inbred rice cultivars,and about 300 inbred rice cultivars are major cultivars（cultivars with a maximum annual planting area of more than one million mu）.Statistics from the National Agricultural Technology Extension and Service Center in 2018 showed that the annual planting area of the major inbred cultivars accounted for more than half of the total annual planting area of inbred rice cultivars.Therefore,inbred rice cultivars play an important role in Chinese rice production.However,after decades of genetic improvement,it is not clear how the major inbred rice cultivars changed,how they responded to the breeding objectives of different periods,and the genetic mechanism of their large-scale cultivation in China overtaking other rice cultivars.In this study,501 inbred rice cultivars,including 356 major inbred rice cultivars bred since the 1950s,78 landraces and 67 introduced germplasms,were used to analyze the genomic variation and evolution of Chinese inbred rice cultivars.The main results are as follows:（1）Fine map of genomic variation of inbred rice cultivars was constructed.Whole genome resequencing was carried out at an average depth of 21.3×.After filtration and quality control,a total of3,010,765 SNPs and 275,077 In Dels were detected in the rice genome.Based on this,a fine map of genomic variation of Chinese inbred rice cultivars was constructed.（2）The genetic contributions of landraces and introduced cultivars to the major inbred rice cultivars bred in various periods were clarified.Based on the population differentiation index F_ST and relative identity by descent（r IBD）,we found the major cultivars of Xian were mainly contributed by Xian landraces.Early-season Geng（EG）and middle-season Geng（MG）were mainly contributed by introduced Geng cultivars,while late-season Geng（LG）bred before 1980 was mainly contributed by Geng landraces.The average value of r IBD was used to evaluate the introgression ratio of those major cultivars bred in each period.We found that with the improvement of rice cultivars,the introgression proportion of major Xian cultivars from Xian landraces decreased from 26%in the 1950s to 14%in the 21^st century,and the introgression from introduced Xian cultivars increased from 1%in the 1950s to 8%in the 21^st century.The introgression proportion of EG and MG from introduced Geng decreased from 29%and 25%in the1950s and 1960s to 25%and 11%in the 21^st century,respectively.The introgression of LG from introduced Geng cultivars increased from 5%in 1950s and 1960s to 10%.The introgression of EG,MG and LG from Geng landraces decreased from 10%,17%and 34%to 6%,7%and 8%,respectively.（3）The evolution of important functional genes in the breeding of major inbred rice cultivars were systematically revealed.By comparing the haplotypes of 54 important functional genes,we found that the favorable haplotypes of eight yield-related genes（including GS3,GS5,CYP78A13,etc.）,five disease resistance and stress tolerance-related genes（including Pi56,Pi-ta,etc.）,seven plant morphology-related genes（including TAC3,HTD1,TAC1,etc.）and three quality-related genes（ALK,Chalk5,Wx）have been artificially selected in the improvement of Xian cultivars.In the improvement of Geng major cultivars,the favorable haplotypes of yield-related gene GS6,eight disease and stress resistance-related genes（including COLD1,HAN1,Pid3,etc.）,plant morphology-related gene NAL1,heading date related genes Hd6 and Hd18,and quality-related genes ALK and Wx have been artificially selected.We found that most of the genes related to yield and plant morphology have not been utilized in Geng.The utilization of genes controlling biotic stress resistance in Xian is stronger than that in Geng,while the utilization of genes controlling cold tolerance and heading date in Geng is stronger than that in Xian.（4）Six candidate genomic regions related to agronomic traits were identified.Through association analysis and selection footprint analysis,the loci RTGW9,RPH1 and RHD6 were identified to control thousand-grain weight,plant height and heading date in Xian,and the loci RHD8,RBRSR4 and RFLW3were identified to be related to heading date,blast resistance spectrum and control the flag-leaf width and grain number per panicle in Geng,respectively.The haplotype analysis showed that the five candidate regions RTGW9,RPH1,RHD6,RHD8 and RBRSR4 were all under artificial positive selection in the genetic improvement of major rice cultivars.（5）The genetic basis of major cultivars different from the minor inbred cultivars was revealed.Using 94 functional genes,211 major inbred cultivars bred since the 1980s and 115 cultivars planted in small area were compared.It was found that Xian was dominant in the favorable haplotypes of plant morphology and biotic stress,and Geng was dominant in the favorable haplotype of heading date and abiotic stress.In Xian,the utilization of four yield-related genes（NOG1,RTGW9,TGW6,LAX1）,seven disease resistance-related genes（Pid2,Pid3,Bph3,etc.）,eight stress tolerance-related genes（HIS1,Os MYB2,Os LG3,etc.）and six heading date-related genes（DTH8,Hd1,Hd17,etc.）made major cultivars superior to minor cultivars.In Geng,the utilization of two yield-related genes（LAX1 and GS6）,six disease resistance-related genes（Pi5-1,RBRSR4,STV11,etc.）,five stress tolerance-related genes（Os PP15,CTB4a and HAN1,etc.）and four heading date-related genes（Hd1,Hd6,RHD8,Hd18）made Geng major cultivars superior to minor cultivars.