Genetic diversity and population structure analysis of 161 broccoli cultivars based on SNP markers

To better understand the genetic diversity and population structure of broccoli cultivars planted in China,a total of 161 representative broccoli cultivars in the past 25 years were collected and analysed based on single nucleotide polymorphism(SNP)markers.Ten pairs of primers with good polymorphism and high resolution were screened from 315 pairs of SNP primers by 3 broccoli accessions(inbred lines)with different phenotypes and maturity.The 10 pairs of SNP primers were selected,producing 78 alleles.The diversity analysis indicated that the polymorphism information content(PIC)of SNP primer ranged from 0.64 to 0.90.The observed number of alleles(Na)was 2.00,the effective number of alleles(Ne)was 1.11–2.00,the Nei’s gene diversity(H)was 0.10–0.50,and Shannon information index(I)was 0.20–0.70 using PopGene32 software.The clustering results showed that the 161 broccoli cultivars could be divided into 4 major subgroups(A,B,C and D),foreign cultivars were all assigned to subgroup A,and domestic cultivars were assigned to 3 subgroups of B,C,and D.This study indicated that some domestic cultivars and foreign cultivars were similar in genetic background,but most domestic cultivars were still different from the Japanese cultivars.When K=2,the population structure result presented that 161 broccoli cultivars could be divided into 1 simple group(2 groups)and 1 mixed group.When Q≥0.6,143(88.82%)broccoli cultivars belonged to the simple groups.In simple groups 68(42.24%)broccoli cultivars of group 1 were derived from Japan,the United States,Switzerland,the Netherlands,China-Taiwan,and China-Mainland;75(46.58%)broccoli cultivars belonged to group 2;when Q<0.6,18(11.18%)broccoli cultivars belonged to the mixed groups.This study is helpful to understand the diversity and resolution of broccoli cultivars from worldwide,which is beneficial to plant breeding and materials innovation.And meanwhile,this result is also used for construction of broccoli fingerprint serving for cultivar identification.

Local adaptive evolution of two distinct clades of Beijing and T families of Mycobacterium tuberculosis in Chongqing:a Bayesian population structure and phylogenetic study

Background:Beijing sub-pedigree 2(BSP2)and T sub-lineage 6(TSL6)are two clades belonging to Beijing and T family of Mycobacterium tuberculosis(MTB),respectively,defined by Bayesian population structure analysis based on 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats(MIRU-VNTR).Globally,over 99%of BSP2 and 89%of TSL6 isolates were distributed in Chongqing,suggesting their possible local adaptive evolution.The objective of this paper is to explore whether BSP2 and TSL6 originated by their local adaptive evolution from the specific isolates of Beijing and T families in Chongqing.Methods:The genotyping data of 16090 MTB isolates were collected from laboratory collection,published literatures and SITVIT database before subjected to Bayesian population structure analysis based on 24-loci MIRUVNTR.Spacer Oligonucleotide Forest(Spoligoforest)and 24-loci MIRU-VNTR-based minimum spanning tree(MST)were used to explore their phylogenetic pathways,with Bayesian demographic analysis for exploring the recent demographic change of TSL6.Results:Phylogenetic analysis suggested that BSP2 and TSL6 in Chongqing may evolve from BSP4 and TSL5,respectively,which were locally predominant in Tibet and Jiangsu,respectively.Spoligoforest showed that Beijing and T families were genetically distant,while the convergence of the MIRU-VNTR pattern of BSP2 and TSL6 was revealed by WebLogo.The demographic analysis concluded that the recent demographic change of TSL6 might take 111.25 years.Conclusions:BSP2 and TSL6 clades might originate from BSP4 and TSL5,respectively,by their local adaptive evolution in Chongqing.Our study suggests MIRU-VNTR be combined with other robust markers for a more comprehensive genotyping approach,especially for families of clades with the same MIRU-VNTR pattern.

COVARIANCE STRUCTURAL ANALYSIS WITH POLYTOMOUS VARIABLES IN SEVERAL POPULATIONS

In this paper, covariance structures with polytomous variables in several populations are analyzed. A computationally efficient multistage procedure is proposed to estimate the thresholds and the covariance structure parameters.Statistical properties of the estimators are derived, and a computer program is implemented to obtain the solution. An artificial example is presented to illustrate the method.