Linkage disequilibrium and haplotype block patterns in popcorn populations

Abstract

Linkage disequilibrium (LD) analysis provides information on evolutionary aspects of the 9 populations and allows selecting populations and single nucleotide polymorphisms (SNPs) for 10 association studies. Recently, haplotype blocks have been used to increase the power of quantitative 11 trait loci detection in genome-wide association studies and the prediction accuracy with genomic 12 selection. The objectives of this study were to compare the degree of LD, the LD decay, the LD 13 decay extent, and the number and length of haplotype blocks in the populations and to elaborate the 14 first LD map for maize, for elucidating if the maize chromosomes also had a pattern of interspaced 15 regions of high and low rates of recombination. We used a biparental temperate population, a 16 tropical synthetic, and a tropical breeding population, genotyped for approximately 75,000 SNPs. 17The level of LD expressed by the r 2 values is surprisingly low (0.02, 0.04, and 0.04), but 18 comparable to some non-isolated human populations. The general evidence is that the synthetic is 19 the population with higher LD. It is not expected a significant advantage of haplotype-based 20 association study and along generations genomic selection due to the reduced number of SNPs in 21 the haplotype blocks (2 to 3). The results concerning LD decay (rapid decay after 5-10 kb) and LD 22 decay extent (along up to 300 kb) are in the range observed with maize inbred line panels. Our most 23 important result is that maize chromosomes had a pattern of regions of extensive LD interspaced 24 with regions of low LD. However, our simple simulated LD map provides evidence that this pattern 25 can reflect regions with differences of allele frequencies and LD level (expressed by D') and not 26 regions with high and low rates of recombination. 27 Keywords: gametic phase disequilibrium; LD map; haplotype blocks; intragenic LD. Introduction Linkage disequilibrium (LD) analysis is important to humans, other animal species, and plants because the results can be used for positional cloning, provide information on rate of recombination, gene conversion, and evolutionary aspects of the populations, including recombination history, mutation, selection, genetic drift, and admixture, and allows selecting populations and single nucleotide polymorphisms (SNPs) for association studies [1]. The most common LD measures are D' and r 2 . The statistic D' is the ratio between D (the difference between products of haplotypes, D = P(AB).P(ab)  P(Ab).P(aB)) and the deviation of the actual gametic frequency from linkage equilibrium [2]. The statistic r 2 is the square of the correlation between the values of alleles at two loci in the same gamete, where D is the covariance [3]. Additional information on historical recombination is provided by the analysis of the haplotype blocks pattern in populations. A haplotype block is a chromosome region in which there are few haplotypes (combinations of alleles of multiple SNPs within a haplotype block) (2-4 per block), and for which the ...

Efficiency of Bayesian quantitative trait loci mapping with full‐sib progeny

“…The genotyping and phenotyping simulation processes used REALbreeding software (available by request). This software has been recently used in studies on genomic selection (Viana, Pereira, Mundim, Piepho, & Silva, 2018), genome‐wide association study (Viana, Mundim, Pereira, Andrade, & Silva, 2017a), QTL mapping (Viana, Silva, Mundim, Azevedo, & Jan, 2017b), population structure (Viana, Valente, Silva, Mundim, & Paes, 2013), and linkage disequilibrium (Andrade, Viana, Pereira, Pinto, & Fonseca, 2019). The software simulates individual genotypes for genes and molecular markers and phenotypes in three steps using user inputs.…”

Factors affecting heterotic grouping with cross‐pollinating crops

“…In general, these studies computed several population genetic statistics, such as PIC, expected heterozygosity, and differentiation index, and included an analysis of molecular variance and distinct methods of grouping, such as cluster analysis, principal component/coordinate analysis, and population structure analysis (Leng et al., 2019; Zhang et al., 2018). The PIC is the average probability of detecting linkage to an index locus (a rare dominant allele, for example) (Botstein, White, Skolnick, & Davis, 1980). This probability is maximized when the allele frequencies are 1/n, where n is the number of alleles (0.375, 0.592593, 0.703125, 0.768, 0.810185, 0.83965, 0.861328, and 0.877915 for 2 to 9 alleles, respectively).…”

“…The genotyping and phenotyping processes of the populations, interpopulation crosses, selfed populations, doubled haploid (DH) lines, and single crosses were simulated using REALbreeding software (available by request). REALbreeding has been used to provide simulated data in studies involving genomic selection (J. M. S. Viana, Pereira, Piepho, & Silva, 2019), GWAS (Pereira, Viana, Andrade, Silva, & Paes, 2018), QTL mapping (J. M. S. Viana, Silva, Mundim, Azevedo, & Jan, 2017), linkage disequilibrium (Andrade, Viana, Pereira, Pinto, & Fonseca, 2019), and population structure (Viana, Valente, Silva, Mundim, & Paes, 2013).…”

Significance of linkage disequilibrium and epistasis on the genetic variances and covariance between relatives in non-inbred and inbred populations

“…This software uses the quantitative genetics theory that was described in the previous sections and in Viana (2004). REALbreeding has been used to provide simulated data in investigations in the areas of genomic selection (Viana et al 2019), GWAS (Pereira et al 2018), QTL mapping (Viana et al 2017b), linkage disequilibrium (Andrade et al 2019), population structure (Viana et al 2013), and heterotic grouping/genetic diversity (Viana et al 2020).…”