Optimal use of SSR markers for varietal identification of upland cotton

Guilherme Da Silva Pereira,Paulo Augusto Vianna Barroso,Ana Luíza Ramos Cazé,Fernanda Oliveira Da Cunha Magalhães,Vanessa Cavalcante Almeida,Michelle Garcia Da Silva,João Luís Da Silva Filho,Lúcia Vieira Hoffmann

doi:10.1590/s0100-204x2015000700007

Abstract

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.

Highlights

The genetic diversity of the genus Gossypium is high among wild and domesticated cotton species.Wild cotton comprises 45 diploid and 5 tetraploid species (Campbell et al, 2010), of which four have been independently domesticated in four different regions worldwide
There is evidence that cotton genetic diversity has been declining in breeding programs (Paterson et al, 2004), which can lead to a reduction in yield gain through breeding, since diversity is required for selection (Campbell et al, 2010)
The highest polymorphic information content (PIC) values (≥0.5) were those calculated for the CIR055, CIR165, and CIR249 loci, and the PIC average was 0.374

Summary

Introduction

The genetic diversity of the genus Gossypium is high among wild and domesticated cotton species. Wild cotton comprises 45 diploid and 5 tetraploid species (Campbell et al, 2010), of which four have been independently domesticated in four different regions worldwide. The tetraploid species, is classified into seven different races: one wild and six domesticated (Lacape et al, 2007). There are constraints related to crossing barriers (Pereira et al, 2012) and mainly to traits largely different from those required for commercial cotton production. For this reason, cotton breeding has usually been performed from a narrow genetic base. Intraspecific polymorphic markers can assist breeders, by displaying relevant genetic diversity among cotton lineages from overlooked germplasm banks, for instance

Objectives

Methods

Results