In this study, genetic structure and diversity analysis of 55 indigenous rice cultivars of Northeast India and 5 indica and 5 japonica test varieties were performed using twenty-two SSR markers comprising 9 random and 13 trait-linked markers, and Zn and Fe content. Assessments of genetic diversity of NE rice using molecular markers has been reported previously (20, 21, 22, 23, 24, 25). Though high genetic diversity was previously shown in the NE rice accessions, reports on micronutrients diversity are scarce. Micronutrient deficiencies to Zn and Fe, constitute the two most common nutrient deficiencies in humans (23, 26, 27), especially in developing countries (28). Although rice is a major staple food for a large part of the world especially in Asia, it has been reported as a poor source of essential micronutrients and vitamins (29). In the current study, relatively high Zn and Fe contents were detected in some of the cultivars. The Fe content in the present study was found to be higher than that of rice cultivars of West Bengal and adjoining areas, though zinc content was lower (23). High Fe content was also previously reported in the Indian cultivars by Brar et al (30). The Zn content was higher and the Fe content was found to be lower than a previous report on local rice germplasm of Tripura state (31). Average Zn and Fe contents in the present study were comparable with a previous report (30, 32). In another report by Verma and Srivastav (33), among some aromatic and nonaromatic Indian rice cultivars, aromatic rice had higher Zn and Fe contents. Interestingly, Zn and Fe contents in the current study was found to be higher than the ones reported by Verma and Srivastav (33). Therefore, to overcome the micronutrient deficiencies, the present study will be helpful for designing crop improvement programs, though more investigations are still needed to further find out higher contents of Zn and Fe since these micronutrients are essential for human health and development.
The NE rice cultivars contain considerable genetic diversity and variable traits which might be good sources for various improvement programs (20). All SSR markers used in the present study were found to be polymorphic. A combination of random and trait-linked markers was utilized since Yadav et al. (34) reported trait-linked markers gave higher value of genetic diversity and Polymorphism Information Content (PIC) in some Indian rice germplasm than random markers, whereas several other workers have shown high genetic diversity in NE rice cultivars using random markers (20, 21, 24). The number of alleles per locus (6.7727) found was higher than the ones reported earlier by Upadhyay et al. (35) (3.96 alleles per locus) and lower than that reported by Choudhury et al. (20) (13.57 alleles per locus). However, it was comparable with 7.9 alleles per locus reported by Das et al. (21). The mean HE and PIC found in the present study showed a high value of heterozygosity index. The mean Fst values for all loci and between the two clusters were found to be 0.7786 and 0.1987 respectively indicating very high genetic differentiation among loci and among the clusters. Based on SSR analysis, there were seventeen highly informative markers (PIC>0.50), viz., RM1, RM154, RM131, RM135, RM72, RM171, RM287, RM3825, RM246, RM260, RM525, RM219, RM223, RM8094, RM493, RM3412 and RM169; two informative markers (PIC between 0.25 and 0.50), RM153, RM125, and RM302; and two slightly informative markers (PIC<0.25), RM315 and RM443 (36, 37).
Population structure analysis using STRUCTURE showed highest ΔK value at K=2 revealing that the studied 65 rice cultivars were grouped into two clusters. The number of the cluster was in agreement to the previous studies: two clusters among 29 varieties of cultivated rice of NE India (20) and two clusters among 6 landraces of North-Western Indian Himalayas (38). Roy et al. (24) have also reported a similar result of K=2, among hill rice of Arunachal Pradesh, NE India, belonging to indica and japonica. In the current study, the identified two main clusters can also be divided into sub-clusters corresponding to state-wise grouping. A similar result of state-wise grouping was also observed in aromatic rice germplasm from North Eastern India (13). According to Evano et al. (39), alpha value closed to zero indicated that most of the individuals were from one population or another, and an alpha value greater than 1 indicated that most individuals were admixed. The observed small alpha value in this study (0.0663) might indicate that most of the individuals originated from one population or another.
In some areas of NE India, rice has been cultivated in shifting or jhum lands which only depend on the Monsoon rain. These cultivars survive in long spells of rainless weather and may be good candidates to look for these variable traits. Other important traits include dark color and aroma in Chakhao rice of Manipur, resistance against blast, resistance to gall midge, deep water tolerance in Baon of Assam, drought resistance in Hmawrhang of Mizoram, etc (15, 40, 41). As evident from the current study, the genetic diversity of indigenous rice cultivars was found to be higher than that of agronomically improved varieties. These results are in agreement to a similar pattern observed for rice varieties of the Eastern Himalayan region of Northeast India (20). The use of such genetic variability in breeding programs is a key factor for crop improvement (42). Among the studied rice cultivars, Nalidhan cultivar of Arunachal Pradesh possessed the highest genetic diversity, followed by Vak and Boleng ammo cultivars. These high genetic diversity cultivars are promising candidates as sources for effective breeding or future rice improvement programs. However, some cultivars such as Moirangphou khonganbi, Moirangphou possessed a low level of genetic diversity suggesting necessary actionsshould be taken on the conservation of these landraces. Cultivars such as Vak, Bogaahoo and Tsulu tsuk possessed high genetic diversity and high Zn concentration. Similarly, Kawnglawng, Jakjatsuk, Yarte, Mezamew, etc possessed high Fe content and high genetic diversity. Nalidhan, the cultivar with the highest genetic diversity also possessed Zn and Fe contents higher than the average observed for these studied populations. Lumre also possessed high genetic diversity, high Zn and average Fe content. The highest Zn containing Badalsali cultivar possessed a lower genetic diversity than the average of all the studied populations. Similarly, the Fazu cultivar with the highest Fe content showed lower genetic diversity than the average of all the studied populations. The present investigation showed that the majority of the cultivars with high genetic diversity had high Zn contents and many cultivars also exhibited high genetic diversity along with high Fe content.