Screening of Indigenous rice by quantitative and molecular characterization for salinity tolerance in Cauvery delta region of Tamilnadu, India.

Genetic diversity using Morpho-Molecular Markers
The reserved seeds of all the twenty-eight rice landraces which were collected from the farmers of different areas, were raised in field condition. Genetic diversity among twenty-eight rice genotypes was analyzed using morphological and molecular marker analysis which revealed significant variability for yield and yield component traits. Based on D2 analysis, genotypes were grouped into six clusters, with maximum inter-cluster distance between cluster II and IV.
Molecular study: The harvested seeds were saline-treated (4 dSm-1) and the seedling samples taken for DNA extraction and genotyping were done. The number of alleles per locus ranged from 76 in RM 10852 to 252 in the case of RM336. The primer pairs RM 10852, RM 223, RM 10793, RM 10772, RM 493, RM 336, RM 8094, RM 8046, RM 342, RM 3412, RM 1287, RM 413, RM 222, RM 8264, RM 10843 generated amplified products due to amplification of more than one locus. The total alleles identified in the twenty-eight genotypes were classified into two categories: a) shared alleles and b) Unique alleles. A total of 1959 shared bands and 19 unique allele variants were generated in the form of amplified products using 15 primers pair. The overall size of the PCR products amplified using fifteen primer pairs ranged from 70 bps to 350 bps.)
Polymorphism Information Content (PIC)
Fifteen SSR markers generated 1959 shared alleles and 19 unique alleles with high PIC values indicating polymorphism. The PIC values revealing allele diversity and frequency among the genotypes varied from 0.2633 in the case of RM 3412 to 0.8576 in the case of RM 8046. Considerably, greater magnitude of PIC value was obtained in the primers RM 8046, RM 493, RM 336,RM 10793 and RM 8094.
Clustering analysis based on Euclidian distance matrix
Clustering analysis based on unweighted pair group method with arithmetic mean (UPGMA) method using DARWIN was separated. Based on this, twenty-eight genotypes under study were grouped into four clusters and twelve sub clusters. The cluster composition is described here under.
Cluster1a: Kuzhiyadichan, Anandanoorsanna, Vellaimilagusamba,Anaikomban.
Cluster 1b: Soolaikuruvai, Thanga samba
Cluster 1c: Kichilisamba
Cluster 1d: Kattuyanam
Cluster 2a: Perumkoomvazhai, Kalyan samba
Cluster 2b: Seempalai
Cluster 2c: Neelan samba, Cochin samba
Cluster 3a: Mapillai samba, Sanna samba, Sivappukavuni
Cluster 3b: Sengalpattu sirumani, Pokkali
Cluster 3c: Vellai poovan, Milagu samba, Poovan samba, Sivappusirumani
Cluster 4a: Picini,Seeraga samba, Kothamallisamba
Cluster 4b: Pachai perumal, Arikavuravi, Poompalai
The study demonstrated substantial genetic variability for grain yield per plant, identified marker-trait associations and relationships among traditional landraces of rice. The results provide insights into the diversity that can be exploited for genetic enhancement of saline tolerant rice varieties.