Analysis of genetic diversity and structure in a genebank collection of red clover (Trifolium pratenseL.) using SSR markers

Abstract

Genetic diversity of a red clover global collection was assessed using 36 simple sequence repeat (SSR) primers representing all seven linkage groups (LGs). The number of fragments amplified ranged from 1 to 6 for all the primers. Primer RCS0060 detected highest number of fragments, whereas four SSRs viz., RCS0899, RCS1594, TPSSR40 and RCS6927 amplified single fragment. Size range of amplicons generated by all the primers varied from 100 to 400 bp. Polymorphism information content values ranged from 0.301 to 0.719 with an average value of 0.605. LG wise diversity analysis showed that LG 3 was most diverse (I = 0.65, Ht = 0.44), whereas LG-1 showed minimum diversity (I = 0.48, Ht = 0.26) for the microsatellites used. Bayesian model-based clustering inferred three genetically distinct populations in the red clover germplasm holding and showed considerable admixture in individuals within clusters. Neighbour-joining analysis showed intermixing of accessions within groups. Principal component analysis plot complemented the clustering shown by Structure and distinguished three populations to greater extent. Analysis of molecular variance showed that 91% of the genetic variation was residing within populations, while 9% variation was among populations. Overall, the results showed that a high level of genetic diversity is prevailing in this worldwide collection of red clover, which can be exploited for its genetic improvement through breeding approaches.

Molecular characterization of red clover genotypes utilizing microsatellite markers

“…PIC values determined in the work of Dias et al (2008) were in the range of 0.64 to 0.85 for the three populations and in the range of 0.70-0.91 for 56 individuals of red clover. Gupta et al (2016) reported SSR PIC values range from 0.301 to 0.719 for red clover genotypes, and Vymyslicky et al (2012) found SSR PIC values to be in the range of 0.4 to 0.86.…”

“…Vymyslicky et al (2012) reported that the number of alleles per locus in red clover ranged from 3 to 8, with an average of 4.4. Gupta et al (2016) determined the lowest value of the average number of alleles per locus in the red clover, which amounted 3.18. PIC values determined in this study were somewhat lower when compared to the results of other authors.…”

“…Dugar and Popov (2013) have studied 15 Ukrainian red clover cultivars and found that the among-group genetic variability of SSR markers was low and that it amounted only 6.9% of the total variability. Gupta et al (2016) analyzed a core collection of red clover which was established by (Kouame and Quesenberry, 1993), and dismantling of the genetic variance using AMOVA showed that most of the genetic diversity was contained within the population (91%), while 9% of genetic variation is accounted for amonggroup variability. Berzina et al (2008) were studying seven diploid red clover cultivars based on six SSRs and found that inter-group variation represented only 2% of the total genetic polymorphism, as well as that Φ ST values (0.006 to 0.043), indicated a low genetic differentiation between varieties.…”

Efficiency of SSR and PawS markers for evaluation of genetic polymorphism among red clover (Trifolium pratense L.) cultivars

“…В источниках литературы и ранее встречались сведения о невысоком уровне генетической изменчивости клевера лугового, выявленном с использованием разных типов молекулярных маркеров (Kongkiatngam et al, 1995;Kölliker et al, 2003). Однако большинство исследователей отмечают значительную вариабельность, причем более высокую внутри сортов и популяций, чем на межпопуляционном уровне (Dias et al, 2008;Gupta et al, 2016).…”

“…Ю. Дугарь и В. Попов с помощью SSR-маркеров выявляли ДНК-полиморфизм между сортами украинской селекции (Dugar, Popov, 2013). Исследовательские группы из Индии и Сербии на основе SSR-маркеров изучали генетическую изменчивость образцов клевера лугового из коллекций разных стран мира (Gupta et al, 2016;Radinovic et al, 2017). В России исследования по изучению ДНК-полиморфизма клевера лугового на основе SSR-маркеров для идентификации и генетической паспортизации селекционных достижений только начинают появляться (Klimenko, Kozlov, 2018; Klimenko et al, 2019).…”