Optimal use of SSR markers for varietal identification of upland cotton

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.Index terms: Gossypium hirsutum, cultivar discrimination, intraspecific polymorphism, microsatellite. Uso otimizado de marcadores SSR para identificação varietal de algodoeiro herbáceoResumo -O objetivo deste trabalho foi identificar marcadores polimórficos de sequências simples repetidas (SSR) para identificação varietal de algodão e avaliação da distância genética entre as variedades. Inicialmente, 92 marcadores SSR foram genotipados em 20 cultivares de algodão do Brasil. Desse total, 38 locos foram polimórficos, dos quais dois deles foram amplificados por um único par de iniciadores; o número médio de alelos por loco foi 2,2. Os conteúdos de informação polimórfica (PIC) e de poder de discriminação (DP) foram, em média, 0,374 e 0,433, respectivamente. A distância genética média foi de 0,397 (mínima de 0,092 e máxima de 0,641). Um painel de 96 variedades originárias de diversas regiões do mundo foi avaliado por 21 locos polimórficos derivados a partir de 17 pares de iniciadores selecionados. Entre essas variedades, a distância genética média foi de 0,387 (mínima de 0 e máxima de 0,786). Os dendrogramas elaborados a partir de média aritmética não ponderada (UPGMA) não refletiram as regiões do Brasil (20 genótipos) ou do mundo (96 genótipos), onde as variedades ou linhagens foram selecionadas. O procedimento de reamostragem bootstrap mostra que a identificação dos genótipos é viável com 19 locos. Os marcadores polimórficos avaliados são úteis na identificação varietal de um painel amplo de variedades de algodão e podem ser aplicados em estudos de diversidade da espécie.Termos para indexação: Gossypium hirsutum, discriminação de cultivares, polimorfismo intraespecífico, microssatélite.

Research Article Genetic diversity of arboreal cotton populations of the Brazilian semiarid: a remnant primary gene pool for cotton cultivars.

“…The genetic diversity of the collection is greater than the shown by breeding lineages (Moiana et al, 2015;Pereira et al, 2015), G. barbadense (Almeida et al, 2009) or G. mustelinum Menezes et al, 2014). The PIC values were also more elevated than those found for cultivars (Yu et al, 2012;Hinze et al, 2015;Moiana et al, 2015) showing discriminative potential conferred by 12 loci.…”

Genetic variability in landraces populations and the risk to lose genetic variation. The example of landrace ‘Kyperounda’ and its implications for ex situ conservation

“…Furthermore, in the case of landraces, Dj varied across loci ranging from 0.63 (WMS260) to 0.99 (WMS268), indicating a very low likelihood of alike genotypes. Hence, it seems that Dj is more appropriate than RP in order to select primers for genetic identification; since it relies on the number of assessed individual genotypes and allows the probability display of randomly-selected individuals’ discrimination by each marker [55].…”

Inter simple sequence repeats and morphological traits to identify cultivated cotton varieties (Gossypium barbadense L.) in Egypt

“…The first step in producing germplasm and crop cultivars is to characterize genetic diversity and the degree of connection between and within genetic resources, which are regarded as sources for new crop varieties (Govindaraj et al 2015;Han et al 2022) and essential for the crop improvement success (Rana et al 2007). Genetic diversity data is vital when attempting to improve crops and develop new varieties (Bakhsh et al 2019;Pereira et al 2015;Swarup et al 2021).…”