Abstract
Fully domesticated rice is considered to have emerged in India at approximately 2000 B.C., although its origin in India remains a contentious issue. The fast-growing 60-days rice strain described in the Vedic literature (1900–500 B.C.) and termed Shashtika (Sanskrit) or Njavara (Dravidian etymology) in Ayurveda texts including the seminal texts Charaka Samhita and Sushruta Samhita (circa 660–1000 B.C.) is a reliable extant strain among the numerous strains described in the Ayurveda literature. We here report the results of the phylogenetic analysis of Njavara accessions in relation to the cultivars belonging to the known ancestral sub-groups indica, japonica, aromatic, and aus in rice gene pool and the populations of the progenitor species Oryza rufipogon using genetic and gene genealogical methods. Based on neutral microsatellite markers, Njavara produced a major clade, which comprised of minor clades corresponding to the genotypic classes reported in Njavara germplasm, and was distinct from that were produced by the ancestral sub-groups. Further we performed a phylogenetic analysis using the combined sequence of 19 unlinked EST-based sequence tagged site (STS) loci with proven potential in inferring rice phylogeny. In the phylogenetic tree also the Njavara genotypic classes were clearly separated from the ancestral sub-groups. For most loci the genealogical analysis produced a high frequency central haplotype shared among most of the rice samples analyzed in the study including Njavara and a set of O. rufipogon accessions. The haplotypes sharing pattern with the progenitor O. rufipogon suggests a Central India–Southeast Asia origin for Njavara. Results signify that Njavara is genetically distinct in relation to the known ancestral sub-groups in rice. Further, from the phylogenetic features together with the reported morphological characteristics, it is likely that Njavara is an extant early domesticate in Indian rice gene pool, preserved in pure form over millennia by the traditional prudence in on-farm selection using 60-days maturity, because of its medicinal applications.
Highlights
Among the numerous rice (Oryza sativa L.) strains described in the seminal Sanskrit compendia of Ayurveda medicine Charaka Samhita (Van Loon, 2003) and Sushruta Samhita (Bhishagratna, 1907) (Ninivaggi, 2010), Shashtika, which is grown in Kerala and known locally by the Dravidian name Njavara (Burrow and Emeneau, 1961; Singh, 1992; Sreejayan et al, 2011), is a reliable extant strain in the present day rice gene pool
The Njavara germplasm used in this study for genetic analysis consisted of 213 genetically distinct individuals including the 42 previously identified individuals (Sreejayan et al, 2011) and the 171 individuals identified in this study (Supplementary Tables 1a, 2). (2) Traditional rice cultivars: We sampled 310 traditional rice cultivars from 14 states encompassing the major rice growing regions in India (Supplementary Table 3a)
In addition to the canonical ancestral sub-groups (Garris et al, 2005), a unweighted pair-group method with arithmetic average (UPGMA) cluster analysis of 589 rice individuals (Figure 1B and Supplementary Figure 1) using the allelic data generated by 70 microsatellite loci (Supplementary Tables 4a, 5a) produced a non-canonical group confined within 170 Njavara individuals belonging to 78 collections (Figure 1B, Supplementary Figure 1 and Supplementary Table 2)
Summary
Among the numerous rice (Oryza sativa L.) strains described in the seminal Sanskrit compendia of Ayurveda medicine Charaka Samhita (Van Loon, 2003) and Sushruta Samhita (Bhishagratna, 1907) (circa 660–1000 B.C.) (Ninivaggi, 2010), Shashtika (or Sastika), which is grown in Kerala and known locally by the Dravidian name Njavara (Burrow and Emeneau, 1961; Singh, 1992; Sreejayan et al, 2011), is a reliable extant strain in the present day rice gene pool. The people of Kerala have ritualistically preserved Njavara over centuries, for its grains are indispensable in the preparation of several acclaimed Ayurveda medicines (Singh, 1992; Sreejayan et al, 2011), the other rice strains described in Ayurveda texts are either extinct or we are unable to recognize them in the present day gene pool (Singh, 1992). Farmers traditionally identify and select Njavara on-farm based on its 60-days maturity (Sreejayan et al, 2011)
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