Assessment of genetic purity in rice (Oryza sativa L.) hybrids using microsatellite markers

Abstract

The objective of the present study is to detect genetic impurity in the seed lots of CMS lines, restorers and hybrids and to identify signature markers to differentiate parents and hybrids through DNA-based assays. Furthermore, attempts have been made to find out an alternative to Grow-Out-Test, which is very tedious, time consuming and used conventionally for seed genetic purity testing since beginning of quality seed multiplication chain. Fifty-one rice-specific sequence tagged microsatellite (STMS) primer pairs distributed throughout the rice genome were employed for fingerprinting of eight rice hybrids and their parental lines with a view to assess variation within parental lines and to test the genetic purity of the commercial seed lots. Among those, 51 markers, 28 microsatellite markers showed polymorphism (54.90 %). A total of 98 alleles were obtained with an average of 1.92 alleles per primer pair and number of alleles amplified for each primer pair ranged from 1 to 4. A set of markers were identified to differentiate parental lines of the hybrids and which emphasizes the immense scope of those molecular markers for their use in the unambiguous identification of hybrid, which would be of great benefit to farmers that depend on the hybrids.

Peer Review #2 of "Hybrid identification for Glycine max and Glycine soja with SSR markers and analysis of salt tolerance (v0.1)"

“…The former, which is relied on the different phenotypic traits of hybrids and their parental lines, is considerably restricted for the limited intuitive agronomical traits, or because some agronomical traits can be detected only in the particular plant growth period, and some traits are very vulnerable to the environmental conditions. The assessment of genetic purity of hybrids via molecular fingerprinting or banding patterns of their parental lines based on SSR markers have been utilized in some crops, such as in maize (Hipi et al, 2013), rice (Bora et al 2016), and barley (Ben Romdhane et al, 2018). In our present study, the similar banding patterns (Figure 3) as Ben Romdhane et al (2018) were observed in the true hybrids, which are co-dominant SSR markers from both parents.…”

New EST-SSR Markers for Individual Genotyping of Opium Poppy Cultivars (Papaver somniferum L.)

“…These analyses were made on many plant species, such as Ambrosia artemisiifolia [36], Vigna unguiculata L. Walp. [37], Brassica oleracea [38], Solanum tuberosum [39], and Oryza sativa L. [40], and demonstrated the versatility of microsatellite markers. The number of SSR markers for the opium poppy is increasing, but they are poorly characterized in most cases; therefore, only a few of them are suitable for variety identification.…”

Utilization of SSR Markers for Seed Purity Testing in Popular Maize Hybrids

“…The SSR markers identified had both female and male specific bands and are useful in genetic purity testing. The use of SSR markers for genetic purity testing has already been demonstrated in maize (Daniel et al, 2012;Mrutu, 2015;Simon and Lovasz, 2016;Wu et al, 2010); rice (Bora et al, 2016;Galal et al, 2014;Moorthy et al, 2011;Sudharani et al, 2013), pearl millet (Nagawade et al, 2016), eggplant (Reddy et al, 2015), soybean (Zhang et al, 2014), cauliflower (Zhao et al, 2012) and in sunflower (Pallavi et al, 2011).…”