Linkage disequilibrium and haplotype block patterns in popcorn populations

Linkage disequilibrium (LD) and haplotype blocks have been a preliminary and powerful knowledge for genomic investigates in humans, animals and plants. We aimed to describe the LD measures, D’ and r 2 , and to characterize haplotype block patterns in popcorn populations (synthetic and breeding population) from tropical and temperate origins (biparental population). Three populations were genotyped by genotyping-by-sequencing (GBS), 190 or 192 individual from each population. After the data quality control the final marker set remaining for analysis ranged from 75,000 to 76,055 SNPs. D’ and r 2 were assessed per chromosome, and haplotype blocks were characterized by number and size of block, and SNP number. LD and haplotype blocks were also evaluated within 12 genes containing polymorphisms related to the biosynthesis of zein, starch, cellulose and fatty acids. Our results showed that the synthetic is the population with higher LD, followed by the biparental population. The lower average D' value in the breeding population reflects its recombination history. We observed low average r 2 values in the populations. There is an initially higher LD decrease for SNPs separated by 51- 100 kb (3 to 7% for D' and 28 to 66% for r 2 , on average) and then a gradual decrease to the minimum LD value for SNPs separated by 451-500 kb. The number and length of the haplotype blocks and the number of SNPs per haplotype block were proportional to the average r 2 . However, it is not expected a significant advantage of haplotype-based association study and along generations genomic selection, due to the reduced number of SNPs in the haplotype blocks (2 to 3). The LD intragenic approach revealed that tropical populations (synthetic and breeding population) developed by breeding program, based on expansion volume, have higher LD and presence of haplotype blocks. However, we cannot infer that the higher r 2 values observed in 11 of the 12 genes are due to selection for quality in populations. Keywords: Gametic Phase Disequilibrium. Haplotypes. Biparental Population. Synthetic. Breeding Population.

Grantor dc:publisher

Universidade Federal de Viçosa

Year dc:date.issued

2019

Author dc:creator

• Andrade, Andréa Carla Bastos

Advisor dc:contributor.advisor

• Viana, José Marcelo Soriano

• Gametas
• Haplótipos
• Genética vegetal
• Milho de pipoca - Populações - Melhoramento genético

Statement dc:rights

• Acesso Aberto

Language dc:language.iso

eng

Repository record dc:identifier.uri

https://locus.ufv.br//handle/123456789/28706

OAI identifier oai:identifier

oai:locus.ufv.br:123456789/28706