Characterization Of Chromosome Variation And Its Effects In Chinese Wheat Evolution

With the rapid development of high throughput sequencing,the identification of genome Structural variation(SV)and genetic mapping have been greatly promoted,and a lot of SVs which had positive effect on phenotype have been identified.However,the current sequencing and assembly techniques are still not easy to develop gapless reference sequences of large and complex genomes,such as wheat,particularly in the tandem repeat-enriched regions like telomeres,centromeres and other heterochromatin regions.Structural chromosome variations(SCVs),including translation,inversion,Indel and duplication,as a kind of large-scale genomic variation play important roles in genome evolution of wheat,can be identified by cytological technique.Meanwhile,chromosome variations frequently occurred in wheat evolution,Therefore,cytological characterization of wheat is necessary for clarifying the types and frequencies of chromosomal variations,identifying predominant variants and their genetic effects,which is important for uncovering and exploiting the rich allelic variations and beneficial gene clusters in wheat and its relatives.In view of the limitations of the method,little knowledge about the structural variations of these chromatins and variations.Oligonucleotide probe fluorescence in situ hybridization,provide new solutions for revealing chromosome variations on a large scale.In this study,the chromosome composition and variation characteristics of Chinese wheat mini-core collection and wheat accessions from Shanxi,China,and two genetic groups,were analyzed by once FISH using the Oligonucleotide probe multiplex#7(Oligonucleotide probe multiplex,ONPM#7)and SCVs combined with genome wide association analysis(GWAS)provide a simple and efficient method for identifying phenotypic effects of SCVs.The main results were as follows:1 Chromosome variations in Chinese wheat mini-core collection2 types of inversion and 20 translation types were detected in 59(22.52%)cultivars of Chinese wheat mini-core collection.Among these rearrangements,the frequency of RT4AS·4AL-1DS/1DL·1DS-4AL(4.58%)was the most,followed by T1RS·1BL,RT1BL·6BS/1BS·6BL and per Inv 6B.The frequency of T1RS·1BL and RT4AS·4AL-1DS/1DL·1DS-4AL increased over the year.Besides structural rearrangements,184 polymorphic types were identified in 262 cultivars.The highest number of polymorphic types was in Chinese landraces(CL)(162),followed by modern Chinese cultivars(MCC)(160),and introduced modern cultivars(IMC)had only 91.There were three evolutionary trends about chromosome polymorphism types.On the whole,chromosomal variation types increased from CL to MCC,some types from landraces were selected during domestication and artificial selection.And chromosome polymorphic information content(CPIC)increased in modern cultivars because of alien introgression and adaption of foreign germplasm.2 Chromosome variations in wheat accessions from Shanxi,China15 types of structural chromosomal rearrangement were detected in 118(41.99%)cultivars.Among these rearrangements,the frequency of T1RS·1BL was the most(26.33%),followed by RT 4AS·4AL-1DS/1DL·1DS-4AL(13.52%).6 and 11 types presented in landrace and modern cultivars,respectively.RT4AS·4AL-1DS/1DL·1DS-4AL present more in dryland wheat,and the frequency of T1RS·1BL in irrigated wheat was significantly higher than that in dryland wheat.T1BL·1RS,RT4AS· 4Al-1DS /1DL· 1DS-4Al increased with year from landraces to modern cultivated.Besides,the main types in chromosomes 2A,6A,1B,2B,5B,7B,and 6D were various between landraces and modern cultivars,and the mean CPIC were higher in cultivars of modern cultivars than the landraces.It can be seen that chromosome variation types adapted to the local environment were selected in the process of domestication of wheat.3 Genome-wide association analysis based on SCVSCVs can be easily recognized and most of them varied in different wheat accessions based on their presence,absence or CNV,which provide a new kind of genetic markers representing large-sale genomic variations.The 281 accessions were then divided into five subgroups.Among them,Landraces were grouped into G2,most T1RS·1BL cultivars were grouped to G4.GWAS analysis identified 29 SCVs with positive effects on 12 phenotypic traits including RT4AS·4AL-1DS/1DL·1DS-4AL conferring higher GT and TGW,and Mg2B-12 with larger effect on GT,GNS,PH,FLW,and TSSN.The number of favored SCVs in modern cultivars were significantly more than that of landraces.4 Genetic transmission and effect analysis of wheat chromosome variationsTo understand the genetic transmission characteristics of chromosome variations in wheat,12 chromosome variations was analyzed using two genetic populations.Segregation distortion of the SCV on the chromosome 4A and 2D were occurred,the frequency of JC-2D and LF-4A were significantly higher than JM-2D and JM-4A,respectively.A recombination happened in the polymorphic signal region of 2A and 3B,and new types of variation were presented.Polymorphic chromosomes showed significant positive effect on phenotype.The SCVs of 4A,5A,6A,6B and 7B,which were Mr4A-7,Mr5A-1,Mr7B-13,Mg2A-3,Mg6B-11,and Mg6A-6 had positive effect on GL,GT,and GW.Among them,the effect of 4 SCVs were validated via GWAS.Further significantly different SNP intervals were identified nearby inversion or polymorphic regions of six variant groups.In the differential SNP regions of two groups on chromosomes 4A,7A and 2D,genes significantly enriched in biological processes functions mainly involved in biosynthetic process,superoxide metabolic process,photosynthetic electron transport in photosystem II,phospholipid metabolic process.Those reflect the effect of SCVs on phenotype and genome differentiation.