Linkage disequilibrium and haplotype block patterns in popcorn populations

Abstract

Linkage disequilibrium (LD) analysis provides information on the evolutionary aspects of populations. Recently, haplotype blocks have been used to increase the power of quantitative trait loci detection in genome-wide association studies and the prediction accuracy of genomic selection. Our objectives were as follows: to compare the degree of LD, LD decay, and LD decay extent in popcorn populations; to characterize the number and length of haplotype blocks in the populations; and to determine whether maize chromosomes also have a pattern of interspaced regions of high and low rates of recombination. We used a biparental population, a synthetic, and a breeding population, genotyped for approximately 75,000 single nucleotide polymorphisms (SNPs). The sample size ranged from 190 to 192 plants. For the whole-genome LD and haplotype block analyses, we assumed a window of 500 kb. To characterize the block and step patterns of LD in the populations, we constructed LD maps by chromosome, defining a cold spot as a chromosome segment including SNPs with the same LDU position. The LD and haplotype block analyses were also performed at the intragenic level, selecting 12 genes related to zein, starch, cellulose, and fatty acid biosynthesis. The populations with the higher and lower frequencies of |D'| values greater than 0.75 were the biparental (65–74%) and the breeding population (26–58%), respectively. There were slight differences between the populations regarding the average distance for SNPs with |D'| values greater than 0.75 (in the range of approximately 207 to 229 kb). The level of LD expressed by the r2 values was low in the populations (0.02, 0.04, and 0.04, on average) but comparable to some non-isolated human populations. The frequency of r2 values greater than 0.75 was lower in the biparental population (0.2–0.5%) and higher in the other populations (0.2–1.6%). The average distance for SNPs with r2 values greater than 0.75 was much higher in the biparental population (approximately 80 to 126 kb). In the other populations, the ranges were approximately 6 to 19 and 6 to 35 kb. The heatmaps for the regions covered by the first 100 SNPs in each chromosome, in each population (1 to 3.3 Mb, approximately), provided evidence that the comparatively few high r2 values (close to 1.0) occurred only for SNPs in close proximity, especially in the synthetic and breeding populations. Due to the reduced number of SNPs in the haplotype blocks (2 to 3) in the populations, it is not expected advantage of a haplotype-based association study as well as genomic selection along generations. The results concerning LD decay (rapid decay after 5–10 kb) and LD decay extent (along up to 300 kb) are in the range observed with maize inbred line panels. The LD maps indicate that maize chromosomes had a pattern of regions of extensive LD interspaced with regions of low LD. However, our simulated LD map provides evidence that this pattern can reflect regions with differences in allele frequencies and LD levels (expressed by |D'|) and not regions...

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.…”

Significance of linkage disequilibrium and epistasis on genetic variances in noninbred and inbred populations

“…This program uses the quantitative genetics theory that was described in the previous sections and in JMS Viana [ 24 ]. REALbreeding has been used to provide simulated data in investigations in the areas of genomic selection [ 27 ], GWAS [ 28 ], QTL mapping [ 29 ], linkage disequilibrium [ 30 ], population structure [ 31 ], and heterotic grouping/genetic diversity [ 32 ].…”

The impact of epistasis in the heterosis and combining ability analyses

“…The simulated data set was generated using the software REALbreeding (available by request). REALbreeding has been used in studies related to genomic selection (Viana et al 2019), GWAS (Pereira et al 2018), QTL mapping (Viana et al 2017), LD (Andrade et al 2019), population structure (Viana et al 2013b), heterotic grouping/genetic diversity (Viana et al 2020), and plant breeding (Viana et al 2013a).…”