| Wheat(Triticum aestivum L.)is one of the most important crops world-wide.Study of the key question and basic genetic theory in wheat breeding is very critical to guarantee the food safety of China.Founder parent with multiple favorable genes have been proved a crucial factor of crop breeding and improved breeding efficiency greatly.According to the pedigree analysis,there are many new cultivars and elite parental lines derived from few founder parents.However,the genetic basis of founder parent is not known well.Thus,it is very helpful to explore the essential genetic composition and effect of founder parents.Bima 4 is both a founder parent in wheat breeding history of China and a widely-planted cultivar in wheat production.Bima 1 is a sister line of Bima 4,which is the most widely-planted cultivar in China.Besides Bima 4 and Bima 1,other four sister lines named Bima 2,3,5,6 are all the general varieties without many progeny and large plant area.All the six lines were bred from the cross Mazhamai and Biyumai,but their performance are very different.What is the essence of the diversity? Analysis of the genetic composition and effect of the six sibling lines,especially the Bima 4 as founder parent and Bima 1 as widely-planted cultivar,is benefit for select elite parent in the future.We used 90 K SNP array scan 124 cultivars,and then the whole genome association with yield-related traits in the study.Firstly,we used the founder parent Bima 4 and its sister lines and parents to reveal the founder parent is an objective existence.Secondly,we used Bima 4 and its derivatives and 17 intermediate parents in the pedigree to reveal the founder parents are not random,it is a regular phenomenon in wheat breeding.And finally,we used 29 parents from different periods of wheat breeding in China to analysis the common characters of phenotype and genome in every period.Then we construct the framework of founder parents based on the important genomic regions in order to provide scientific basis for breeding in the future.The main results are as follows:1.Association mapping of yield-related traits with SNP markers.All the 124 cultivars were planted in Yangling,Tai’an,Shijiazhuang,Yangzhou and Chengdu for three consecutive years with three replicates and observed eight traits,such as plant height,heading date,grain number per plant,spike number per plant,spike length,1000-grain weight,spikelet number per spike and sterile spikelet.We used 8331 SNP markers,combined with eight important traits phenotypic data via BLUP analysis to detect the marker-trait-associations(MTAs)by TASSEL software with MLM model.To minimize the false-positive associations,only the genomic regions that marker spacing less than 6cM with p<0.05 as significant threshold were considered as the significant regions.Finally,we have detected 93 important genomic regions controlled eight yield-related traits respectively.There are 58 QTL regions associated with multi traits.All these yield-related regions were mainly distributed on the homologous group 2 and 5.Among these regions,there are 32 QTLs controlled plant height,31 QTLs for TGW,30 QTLs for GNS etc.Otherwise,we determined 35 genomic regions of Bima 4 with favorable alleles which could improve the effect of traits and were worth paying more attention in the following study.2.The founder parent is objective existence in breeding.Explore the principal characteristics of Bima 4 as founder parent by compared with the yield-related traits and genomic characteristic of Bima 4 and its parents,5 sister lines.Compared to its sister lines,the founder parent Bima 4 showed an better performance and a moderate level of yield components at grain number per spike(43.53),1000-grain weight(34.53 g)and spike number per plant(12.17).And the Bima 1 is more prominent than Bima 4,like the 1000-grain weight is slightly higher(35.88 g),the grain number per spike is higher(44.79)and the effective tillers less(11.15).The other 4 lines are defective that can not be founder parents.We used 8331 SNPs which were polymorphism between the parents Mazhamai and Biyumai to analysis the genetic differentiations of Bima 1-6.In general,Bima 4 inherited more genetic components from Mazhamai like Bima 1,2,5,6,but the Bima 3 is on the contrary.Furthermore,we found that Bima 4 have 724 unique alleles more than its sister lines except Bima 3(728 alleles),that implied that Bima 4 as founder parent had more genetic diversity.According to the consensus map of wheat 90 K SNP chip published,these unique alleles tend to concentrate on 21 chromosomes,formed 13 important chromosomal regions.Among them,11 regions associated with yield-related traits.Bima 1 as the widely-planted cultivar,which has 409 unique alleles formed 11 special regions and 6 regions associated yield-related traits,also less than Bima 4.3.The founder parent is a regular phenomenon in wheat breeding.Through the analysis of the genetic of Bima 4 and its 74 derivatives,we detected that the principal characteristics of Bima 4 have been selected in the progeny.Study of the principal phenotypic characteristics of Bima 4 in its derivatives indicated that main yield components of Bima 4 have been inherited to the progeny in four generations,and had produced prominent contributions to its progeny.From the first generation to the fourth generation,the 1000-grain weight was increased from 37.6 g to 41.2 g,the grain number per spike was increased from 41.5 to 46.11,the effective tiller number were reduced from 11.2 to 9.97,and the plant height reduced about 10 cm every generation.In a word,the yield factors of the Bima 4 progeny became more optimum and improved yield gradually.We also analysis the selected regions of Bima 4 in its four generations.The results indicated that the frequency of Bima 4-type alleles at BM4-S5,S6,S9,S11,S12 in its four generations is higher than other regions,especially the favorable alleles.There are three kinds of transfer model of these regions:(1)the favorable alleles were completely transfer to the progeny,the frequency is more than 0.5,such as the BM4-S12;(2)the unfavorable alleles of Bima 4 was replaced by the intermediate parent,such as the BM4-S7;(3)the new regions recombination of Bima 4 and the intermediate parent,like the BM4-S6 controlled GNS with the effect-3.509,and turn to 3.509 after recombined with Early premium.All the results indicated that the founder parent is not random.In addition,16 QTLs regions among the 35-Bima 4 favorable QTLs were selected in its derivatives with the frequency more than 60%.4.The characteristics of founder parent in three periods of wheat breeding in China.Combined with of traits and whole genome SNP analysis of 29 parents from three periods including the 1950-60’S,1970-90’S and after 2000 reveal the characteristic of each period.Phenotype indicated that the characteristic factors of each period changed according to the development of wheat improvement,and the performance is better than the main varieties in the same period.For example,the founder parents in the 1950-60’S are mainly present higher plant height with average 119.31 cm,the lower 1000-grain weight with 31.8 g and the more tillers with average 11.79.But the parents in the year after 2000,the plant height was reduced to 79 cm,the spike number per plant was reduced to 8.89 and the 1000-grain weight increased to 42.5 g.And we also determined the common genomic regions of every period by the same method used in Bima 4 section.There are 11 genomic regions of the founder parents in the year 1950-60’S,20 regions of the 1970-90’S and 61 regions of the year after 2000.These common genomic regions would assist in improving the efficiency of wheat breeding programs.5.We used the common characteristic of founder parents from 2000’S,and the BM4-S5,S6,S9,S11 and S12 and Bima 4 favorable QTLs with the higher selected frequency to formed the framework.The framework consist of important genomic regions could be used to predict the candidate founder parents for coming breeding. |
