The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the world. The efforts for conservation of rice germplasm in NE India should consider saving rice varieties representing different types with specific emphasis given to sali and jum types. The protection against the loss of vast genetic diversity found in indigenous rice varieties in NE India is crucial for maintaining future food security in the changing world.Electronic supplementary materialThe online version of this article (doi:10.1186/2193-1801-2-228) contains supplementary material, which is available to authorized users.

Classical models suggest that recombination rates on sex chromosomes evolve in a stepwise manner to localize sexually antagonistic variants in the sex in which they are beneficial, thereby lowering rates of recombination between X and Y chromosomes. However, it is also possible that sex chromosome formation occurs in regions with pre-existing recombination suppression. To evaluate these possibilities, we constructed linkage maps and a chromosome-scale genome assembly for the dioecious plant Rumex hastatulus. This species has a polymorphic karyotype with a young neo-sex chromosome, resulting from a Robertsonian fusion between the X chromosome and an autosome, in part of its geographic range. We identified the shared and neo-sex chromosome using comparative genetic maps of the two cytotypes. We found that sex-linked regions of both the ancestral and the neo-sex chromosome are embedded in large regions of low recombination. Furthermore, our comparison of the recombination landscape of the neo-sex chromosome to its autosomal homologue indicates that low recombination rates mainly preceded sex linkage. These patterns are not unique to the sex chromosomes: all chromosomes were characterized by massive regions of suppressed recombination spanning most of each chromosome. This represents an extreme case of the periphery-biased recombination seen in other systems with large chromosomes. Across all chromosomes, gene and repetitive sequence density correlated with recombination rate, with patterns of variation differing by repetitive element type. Our findings suggest that ancestrally low rates of recombination may facilitate the formation and subsequent evolution of heteromorphic sex chromosomes.

1Summary 6 Classical models suggest recombination rates on sex chromosomes evolve in a stepwise manner to 7 localize the inheritance of sexually antagonistic variation in the sex where it is beneficial, thereby 8 lowering rates of recombination between X and Y chromosomes. However, it is also possible that sex 9 chromosome formation occurs in regions with pre-existing recombination suppression. To evaluate 10 these possibilities, we constructed linkage maps and a chromosome-scale genome assembly for the 11 dioecious plant Rumex hastatulus, a species with a young neo-sex chromosome found in part of its 12 geographical range. We found that the ancestral sex-linked region is located in a large region 13 characterized by low recombination. Furthermore, comparison between the recombination landscape 14 of the neo-sex chromosome and its autosomal homologue indicates that low recombination rates 15 preceded sex linkage. Our findings suggest that ancestrally low rates of recombination have facilitated 16 the formation and evolution of heteromorphic sex chromosomes. 17

Gymnocladus assamicus is a critically endangered tree species endemic to northeastern India. Local inhabitants traditionally used this species for a variety of purposes. However, rapid population declines led to the species being considered extinct, until fieldwork in 2004 to 2007 identified 14 discrete populations of 1 to 7 trees each. To overcome constraints on field surveys imposed by the region's remoteness and rugged terrain, we targeted areas of further field inventories by estimating the potential distribution of the species. Ecological niche modeling enabled us to identify 26 sites which the model predicted to be highly suitable for the species' occurrence. We conducted rapid field surveys at 14 of the most accessible of these predicted sites. New populations were discovered at 5 of the 14 surveyed sites. In the remaining 12 less accessible sites, we interviewed residents from nearby villages and obtained indirect evidence of populations at 5 additional sites, which remain to be confirmed by direct field observations. This study demonstrates the utility of niche modeling as a tool for locating new populations of rare and endangered species. Our results will enhance ongoing efforts towards in situ conservation of this endangered species.

There is currently a small number of classes of antifungal drugs, and these drugs are known to target a very limited set of cellular functions. We derived a set of approximately 900 nonessential, transactivator-defective disruption strains from the tetracycline-regulated GRACE collection of strains of the fungal pathogen Candida albicans. This strain set was screened against classic antifungal drugs to identify gene inactivations that conferred either enhanced sensitivity or increased resistance to the compounds. We examined two azoles, fluconazole and posaconazole; two echinocandins, caspofungin and anidulafungin; and a polyene, amphotericin B. Overall, the chemogenomic profiles within drug classes were highly similar, but there was little overlap between classes, suggesting that the different drug classes interacted with discrete networks of genes in C. albicans. We also tested two pyridine amides, designated GPI-LY7 and GPI-C107; these drugs gave very similar profiles that were distinct from those of the echinocandins, azoles, or polyenes, supporting the idea that they target a distinct cellular function. Intriguingly, in cases where these gene sets can be compared to genetic disruptions conferring drug sensitivity in other fungi, we find very little correspondence in genes. Thus, even though the drug targets are the same in the different species, the specific genetic profiles that can lead to drug sensitivity are distinct. This implies that chemogenomic screens of one organism may be poorly predictive of the profiles found in other organisms and that drug sensitivity and resistance profiles can differ significantly among organisms even when the apparent target of the drug is the same.