Genetic diversity and population structure of sweet orange [Citrus sinensis (L.) Osbeck] germplasm of India revealed by SSR and InDel markers

Abstract

Sweet orange (Citrus sinensis (L.) Osbeck) is an important commercial citrus fruit crop, cultivated in India and across the world. In India most of the cultivated sweet orange species were introduced varieties. In this study, we used two molecular markers, SSR and InDels, to understand the genetic diversity and population structure of seventy-two sweet orange genotypes. Genetic parameters consisted of a total number of alleles, a number of polymorphic alleles (effective alleles); genetic diversity (G.D.), expected heterozygosity (He), and the polymorphic information content (PIC) were calculated based on molecular data. Two dendrograms were constructed based on the InDels and SSR. In both the cases, they formed three major clusters showing various degrees of variations with respect to members of the clusters. Population structure analysis revealed the presence of two distinct subpopulations. Therefore, in order to address various challenges and develop sweet orange varieties with desirable traits, there is a need to broaden the genetic base of sweet orange through the intensive collection in the northeastern region. These results of intraspecific genetic variability of the collections will dictate the path for the sweet orange breeding and conservation programs in India.

GENETIC DIFFERENTIATION OF CULTIVATED CITRUS FRUITS (Citrus spp.) IN COLOMBIA USING SSR MOLECULAR MARKERS

“…Group VII included Eureka lime (hybrid between C. aurantium × C. medica) and Rangpur lime (hybrid between C. reticulata × C. medica) with a dissimilarity index of 0.759, which showed closer genetic relationships with acid limes and a high genetic differentiation with the rest of the citrus populations. These results agree with those obtained by Nicolosi et al (2000) and Kumar et al (2022), who found close phylogenetic relationships between C. medica, C. aurantifolia, and C. limon. The PCoA principal coordinate analysis in the first three coordinates explained 62.44 % of the total variability of the 19 citrus populations (Figure 2).…”

Application of RAPD Molecular Technique to Study the Genetic Variations of Citrus in South Sulawesi, Indonesia

“…One of Indonesia's leading horticultural commodities is fruit, and Indonesia has local superior citrus species and varieties that are spread throughout the archipelago. Citrus is one of the world's major fruit crops [3], grown in many regions [4], which has high economic value [5]. Citrus fruits belong to the family Rutaceae and subfamily Aurantioideae and can be grown in tropical and sub-tropical climates [6].…”