Genetic Diversity and Genetic Structure of Maize Inbred Lines from Yunnan Revealed by SNP Chips

[Objectives]The genetic diversity and population genetic structure of 107 inbred lines of maize in Yunnan were analyzed,in order to provide technical support for maize germplasm innovation,genetic improvement of germplasm resources,variety management,and lay a solid foundation for exploring genes related to fine traits in the future.[Methods]The 107 maize inbred lines generalized in Yunnan were selected,and 45 backbone inbred lines commonly used in China were used as reference for heterotic group classification.On Axiom Maize 56K SNP Array platform,maize SNP chips(56K)were used to scan the whole maize genome,and the NJ-tree model of Treebest was used to construct a phylogenetic tree.Principal component analysis(PCA)was conducted by GCTA(genome-wide complex trait analysis)to reveal the genetic diversity and population genetic structure.[Results]In the 107 Yunnan local inbred lines,5533 uniformly distributed high-quality SNP marker sites were finally detected.Based on the analysis of these SNP marker sites,Nei s gene diversity index(H)of 107 maize germplasm genes was 0.2981-0.5000 with an average value being 0.4832,and polymorphism information content(PIC)values were 0.2536-0.3750 with an average value being 0.3662.The minimum allele frequency value was 0.5000-0.8178 with an average value being 0.5744.The analysis of population genetic structure showed that when K=6,the maximum value of△K was the maximum,which meant that the inbred lines used in this study could be divided into six groups.They were Tangsi Pingtou blood relationship group,PB blood relationship group,335 female blood relationship group,Zi 330 and the Lüda Honggu blood relationship group,unknown group 1 and unknown group 2.No inbred lines were divided into other heterotic groups.Among them,37 inbred lines from the 2 unknown groups could not be classified into the same group as the 10 known heterotic groups in China.The results of principal component analysis showed that the 107 maize inbred lines generalized in Yunnan could be clearly distinguished from the backbone maize inbred lines commonly used in China.Most of the maize inbred lines in Yunnan were concentrated near the reference backbone inbred lines.But some Yunnan inbred lines were far away from the reference inbred lines commonly used in China.[Conclusions]The maize germplasm resources in Yunnan area were rich in genetic diversity,including multiple heterotic groups,and there was a rich genetic basis of breeding parents.They could be clearly distinguished from the backbone inbred lines commonly used in China,and some of them had a long genetic distance from the backbone inbred lines.The resources which have good application potential can be used to create new heterotic groups.

Identification of genetic loci for grain yield-related traits in the wheat population Zhongmai 578/Jimai 22

The identification of stable quantitative trait locus(QTL)for yield-related traits and tightly linked molecular markers is important for improving wheat grain yield.In the present study,six yield-related traits in a recombinant inbred line(RIL)population derived from the Zhongmai 578/Jimai 22 cross were phenotyped in five environments.The parents and 262 RILs were genotyped using the wheat 50K single nucleotide polymorphism(SNP)array.A high-density genetic map was constructed with 1501 non-redundant bin markers,spanning 2384.95 cM.Fifty-three QTLs for six yield-related traits were mapped on chromosomes 1D(2),2A(9),2B(6),2D,3A(2),3B(2),4A(5),4D,5B(8),5D(2),7A(7),7B(3)and 7D(5),which explained 2.7-25.5%of the phenotypic variances.Among the 53 QTLs,23 were detected in at least three environments,including seven for thousand-kernel weight(TKW),four for kernel length(KL),four for kernel width(KW),three for average grain filling rate(GFR),one for kernel number per spike(KNS)and four for plant height(PH).The stable QTLs QKl.caas-2A.1,QKl.caas-7D,QKw.caas-7D,QGfr.caas-2B.1,QGfr.caas-4A,QGfr.caas-7A and QPh.caas-2A.1 are likely to be new loci.Six QTL-rich regions on 2A,2B,4A,5B,7A and 7D,showed pleiotropic effects on various yield traits.TaSus2-2B and WAPO-A1 are potential candidate genes for the pleiotropic regions on 2B and 7A,respectively.The pleiotropic QTL on 7D for TKW,KL,KW and PH was verified in a natural population.The results of this study enrich our knowledge of the genetic basis underlying yield-related traits and provide molecular markers for high-yield wheat breeding.

A genome scan of recent positive selection signatures in three sheep populations

Domesticated sheep have been exposed to artificial selection for the production of fiber, meat, and milk as well as to natural selection. Such selections are likely to have imposed distinctive selection signatures on the sheep genome. Therefore, detecting selection signatures across the genome may help elucidate mechanisms of selection and pinpoint candidate genes of interest for further investigation. Here, detection of selection signatures was conducted in three sheep breeds, Sunite （n=66）, German Mutton （n=159）, and Dorper （n=93）, using the Illumina OvineSNP50 Genotyping BeadChip array. Each animal provided genotype information for 43 273 autosomal single nucleotide polymorphisms （SNPs）. We adopted two complementary haplotype-based statistics of relative extended haplotype homozygosity （REHH） and the cross-popu- lation extended haplotype homozygosity （XP-EHH） tests. In total, 707,755, and 438 genomic regions subjected to positive selection were identified in Sunite, German Mutton, and Dorper sheep, respectively, and 42 of these regions were detected using both REHH and XP-EHH analyses. These genomic regions harbored many important genes, which were enriched in gene ontology terms involved in muscle development, growth, and fat metabolism. Fourteen of these genomic regions overlapped with those identified in our previous genome-wide association studies, further indicating that these genes under positive selection may underlie growth developmental traits. These findings contribute to the identification of candidate genes of interest and aid in understanding the evolutionary and biological mechanisms for controlling complex traits in Chinese and western sheep.

Genome-wide association study of the backfat thickness trait in two pig populations

Backfat thickness is a good predictor of carcass lean content,an economically important trait,and a main breeding target in pig improvement.In this study,the candidate genes and genomic regions associated with the tenth rib backfat thickness trait were identified in two independent pig populations,using a genome-wide association study of porcine 60K SNP genotype data applying the compressed mixed linear model(CMLM)statistical method.For each population,30 most significant single-nucleotide polymorphisms(SNPs)were selected and SNP annotation implemented using Sus scrofa Build 10.2.In the first population,25 significant SNPs were distributed on seven chromosomes,and SNPs on SSC1 and SSC7 showed great significance for fat deposition.The most significant SNP(ALGA0006623)was located on SSC1,upstream of the MC4R gene.In the second population,27 significant SNPs were recognized by annotation,and 12 SNPs on SSC12 were related to fat deposition.Two haplotype blocks,M1GA0016251-MARC0075799 and ALGA0065251-MARC0014203-M1GA0016298-ALGA0065308,were detected in significant regions where the PIPNC1 and GH1 genes were identified as contributing to fat metabolism.The results indicated that genetic mechanism regulating backfat thickness is complex,and that genome-wide associations can be affected by populations with different genetic backgrounds.