The potentiality of rice microsatellite markers in assessment of cross-species transferability and genetic diversity of rice and its wild relatives

Abstract

The main aim of this study is to assess the potentiality of SSR markers for the identification of the cross-species transferability frequency in a large set of the diverse genome types of wild relative rice along with cultivated rice. Here, we used 18 different rice genotypes representing nine different genome types with 70 SSR markers to investigate the potentiality of cross-species transferability rate. The overall cross-species transferability of SSR markers across the 18 rice genotypes ranged from 38.9% (RM280 and RM447) to 100% (RM490, RM318, RM279, RM18877 and RM20033, RM19303) with an average of 76.58%. Also, cross-species transferability across chromosome ranged from 54.4% (chromosome 4) to 86.5% (chromosome 2) with an average of 74.35%. The polymorphism information content of the markers varied from 0.198 (RM263) to 0.868 (RM510) with a mean of 0.549 ± 0.153, showing high discriminatory power. The highest rate of cross-transferability was observed in O. rufipogon (97%), The highest rate of cross-species transferability was in O. rufipogon (97.00%), followed by O. glaberrima (94.20%), O. nivara (92.80%), Swarna (92.80%), O. longistaminata (91.40%), O. eichingeri (90%), O. barthii (88.50%), O. alta (82.80%), O. australiensis (77.10%), O. grandiglumis (74.20%), O. officinalis (74.20%), Zizania latifolia (70.00%), O. latifolia (68.50%), O. brachyantha (62.80%), Leersia perrieri (57.10%) and O. ridleyi (41.40%) with least in O. coarctata (28.50%). A total of 341 alleles from 70 loci were detected with the number of alleles per locus ranged from 2 to 12. Based on dendrogram analysis, the AA genome groups was separated as distinct group from the rest of the genome types. Similarly, principal coordinate analysis and structure analysis clearly separated the AA genome type from the rest of the genome types. Through the analysis of molecular variance, more variance (51%) was observed among the individual, whereas less (14%) was observed among the population. Thus, our findings may offer a valuable resource for studying the genetic diversity and relationship to facilitate the understanding of the complex mechanism of the origin and evolutionary processes of different Oryza species and wild relative rice.

MOLECULAR GENETIC DIVERSITY IN GREENGRAM (Vigna radiata (L.) Wilczek)

“…The number of alleles produced by above markers ranged from two to five with an average of 2.47 alleles per marker which indicates the high level of genetic diversity. The average number of alleles in this study was more than that of many other species viz., 2.3 alleles in greengram (Gupta et al, 2013), 1.5 alleles in greengram (Kumar et al, 2001), 2.2 alleles in cowpea (Devi and Jayamani, 2020) and 2.87 alleles in mungbean (Ngangkham et al, 2019). The highest number of alleles (5) was recorded by CEDG 097 and CEDG 154 whereas, lowest number of alleles (2) was observed by CEDG 133, CEDG 171 and DMB SSR 014.…”

Microsatellite Content in 397 Nuclear Exons and Their Flanking Regions in the Fern Family Ophioglossaceae

“…Additionally, mutations in the flanking regions (or in the microsatellites) may lead to homoplasy (if the scoring is focused only on the fragment length) [ 10 , 11 ]. Additional issues may be related to the primer design and their transferability across related and, especially, more distant species [ 12 , 13 ].…”