Wild Relatives Of Rice Research Articles

Analysis of natural variation of the rice blast resistance gene Pike and identification of a novel allele Pikg.

Plant major resistance (R) genes are effective in detecting pathogen signal molecules and triggering robust defense responses. Investigating the natural variation in R genes will allow identification of the critical amino acid residues determining recognition specificity in R protein and the discovery of novel R alleles. The rice blast resistance gene Pike, comprising of two adjacent CC-NBS-LRR genes, namely, Pike-1 and Pike-2, confers broad-spectrum resistance to Magnaporthe oryzae. Here, we demonstrated that Pike-1 determined Pike-specific resistance through direct interaction with the pathogen signal molecule AvrPik. Analysis of natural variation in 79 Pike-1 variants in the Asian cultivated rice Oryza sativa and its wild relatives revealed that the CC and NBS regions, particularly the CC region of the Pike-1 protein were the most diversified. We also found that balancing selection had occurred in O. sativa and O. rufipogon to maintain the genetic diversity of the Pike-1 alleles. By analysis of amino acid sequences, we identified 40 Pike-1 variants in these rice germplasms. These variants were divided into three major groups that corresponded to their respective clades. A new Pike allele, designated Pikg, that differed from Pike by a single amino acid substitution (D229E) in the Pike-1 CC region of the Pike protein was identified from wild rice relatives. Pathogen assays of Pikg transgenic plants revealed a unique reaction pattern that was different from that of the previously identified Pike alleles, namely, Pik, Pikh, Pikm, Pikp, Piks and Pi1. These findings suggest that minor amino acid residues in Pike-1/Pikg-1 determine pathogen recognition specificity and plant resistance. As a new blast R gene derived from rice wild relatives, Pikg has potential applications in rice breeding.

Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species

Wild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a “genetic reservoir” for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.

Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species

Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species Oryza sativa ssp. japonica. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, REGULATOR OF AWN ELONGATION 1 (RAE1) and RAE2. To understand the conserveness of RAE1 and RAE2 in wild rice relatives, we analyzed RAE1 and RAE2 sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional RAE1 and RAE2, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of RAE1 and RAE2 were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of RAE1 and RAE2 were selected after the speciation of O. sativa, and that two-step loss of function in RAE1 and RAE2 contributed to awnlessness in Asian cultivated rice.

Status of the Ex Situ and In Situ Conservation of Brazilian Crop Wild Relatives of Rice, Potato, Sweet Potato, and Finger Millet: Filling the Gaps of Germplasm Collections

This study presents the status of ex situ and in situ conservation for the crop wild relatives of rice, potato, sweet potato, and finger millet in Brazil, and the subsequent germplasm collection expeditions. This research is part of a global initiative entitled “Adapting Agriculture to Climate Change: Collecting, Protecting, and Preparing Crop Wild Relatives” supported by the Global Crop Diversity Trust. Species of the primary, secondary, and tertiary gene pools with occurrences reported in Brazil were included: Oryza alta Swallen, O. grandiglumis (Döll) Prod., O. latifolia Desv., O. glumaepatula Steud., Eleusine tristachya (Lam.) Lam., E. indica (L.) Gaertn., Solanum commersonii Dunal, S. chacoense Bitter, Ipomoea grandifolia (Dammer) O’Donell, I. ramosissima (Poir.) Choisy, I. tiliacea (Willd.) Choisy, I. triloba L., and I. cynanchifolia Meisn. The status of the ex situ and in situ conservation of each taxon was assessed using the gap analysis methodology, and the results were used to plan 16 germplasm collection expeditions. Seeds of the collected material were evaluated for viability, and the protocols for seed germination and cryopreservation were tested. The final conservation score, resulting from the gap analysis and including the average of the ex situ and in situ scores, resulted in a classification of medium priority of conservation for all the species, with the exception of I. grandifolia (high priority). The total accessions collected (174) almost doubled the total accessions of these crop wild relatives incorporated in Embrapa’s ex situ conservation system prior to 2015. In addition, accessions for practically absent species were collected for the ex situ conservation system, such as Ipomoea species, Eleusine indica, and Solanum chacoense. The methods used for dormancy breaking and low temperature conservation for the Oryza, Eleusine, and Ipomoea species were promising for the incorporation of accessions in the respective gene banks. The results show the importance of efforts to collect and conserve ex situ crop wild relatives in Brazil based on previous gap analysis. The complementarity with the in situ strategy also appears to be very promising in the country.

Recanvassing of Select Wild Rice (Oryza spp.) in the Philippines

Wild rice relatives (WRRs) have been used by breeders to draw genes needed to develop varieties that are resistant to pests and diseases and can adapt to adverse environments, especially to climate change. This study was conducted to reassess the presence of WRRs in their natural habitats. A total of 14 WRR were collected: three samples of O. meyeriana, nine samples of O. minuta, and two samples of O. rufipogon from Luzon, Visayas, and Mindanao. In comparison with previous recollection and recanvassing mission and deposited WRR at the International Rice Research Institute (IRRI) Genetic Resources Center (GRC), we see the existence of O. meyeriana population in new sites in Salong and Magballo, Kabankalan in Negros Occidental, Visayas while O. minuta confirms previously identified natural habitat in Pangil, Laguna in Luzon; however, new sites were identified in Magballo, Kabankalan, Negros Occidental. O. rufipogon populations were still found in Lake Apo, as previously reported but limited publication on the populations found in Lake Napalit – both in Bukidnon, Mindanao. Further study is needed to characterize the existing WRRs and expand the recanvassing sites to develop a more holistic conservation program in support to pre-breeding programs

Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice.

As the world’s population expands from 7.6 billion to 10 billion over the next 30 years, scientists and farmers across the globe must explore every angle necessary to provide a safe, stable and sustainable food supply for generations to come. Rice, and its wild relatives in the genus Oryza, will play a significant role in helping to solve this 10 billion people question due to its place as a staple food for billions. The genus Oryza is composed of 27 species that span 15 million years of evolutionary diversification and have been shown to contain a plethora of untapped adaptive traits, e.g., biotic and abiotic resistances, which can be used to improve cultivated rice. Such traits can be introduced into cultivated rice, in some cases by conventional crossing, and others via genetic transformation and gene editing methods. In cases where traits are too complex to easily transfer to cultivated rice [e.g., quantitative trait loci (QTL)], an alternative strategy is to domesticate the wild relative that already contains the desired adaptive traits – i.e., “neodomestication”. To utilize the Oryza genus for crop improvement and neodomestication, we first need a set of genomic resources that can be used to efficiently identify, capture, and guide molecular crop improvement. Here, we introduce the concept of platinum standard reference genome sequences (PSRefSeq) – a new standard by which contiguous near-gap free reference genomes can now be produced. By having a set of PSRefSeqs for every Oryza species we set a new bar for how crop wild relatives can be integrated into crop improvement programs.

Morphological characterization and genetic identity of crop wild relatives of rice (Oryza sativa L.) collected from different ecological niches of India

Crop wild relatives of rice (Oryza sativa L.) are an important reservoir of genes for broadening the genetic base of commercial varieties. India is the centre of genetic diversity of some of the wild as-well-as the cultivated rice species. In order to collect genetic diversity, explorations were undertaken in six states located in different agro-ecological zones of India. Forty-four accessions belonging to four wild species (Oryza rufipogon Griff., Oryza nivara Sharma et Shastry, Oryza officinalis Wall. ex Watt and Oryza sativa L. f. spontanea Roshev.) including two accessions of cultivated rice (Oryza sativa L. subsp. indica Kato) were collected from different ecological niches. The rice accessions were characterized using 28 morphological descriptors, which included 15 qualitative and 13 quantitative traits. Wild rice accessions displayed a broad range of phenotypic variation for plant height, main heading days, days to 50% flowering, flag-leaf length and width, panicle shape and size, peduncle length, awning pattern, awn length and colour, seed length and width, seed length/width ratio and 100-seed weight. Cluster analysis based on Jaccard’s similarity coefficients derived from 28 morphological traits grouped 44 accessions into three clades. DNA sequencing revealed that internal transcribed spacer (ITS) region of 18S–5.8S–28S nuclear ribosomal cistron varied from 574 to 577 bp with mean of 576.1 bp in AA-genome species. GC content was high in ITS region, which varied from 69.57 to 70.36% with mean value of 69.99%. Neighbour-joining phylogenetic tree distinguished Oryza sativa–nivara–rufipogon complex from other species of AA-genome. The wild germplasm characterized in this study could be utilized in the genetic enhancement of cultivated rice.

Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating-system evolution.

Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage‐specific gene families associated with the self‐incompatibility (SI) and formation of reproductive separation. We show how lineage‐specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage‐specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome‐wide expansion of genes encoding NBS‐LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata.

Evaluation of rice wild relatives as a source of traits for adaptation to iron toxicity and enhanced grain quality.

Rice wild relatives (RWR) constitute an extended gene pool that can be tapped for the breeding of novel rice varieties adapted to abiotic stresses such as iron (Fe) toxicity. Therefore, we screened 75 Oryza genotypes including 16 domesticated O. sativa genotypes, one O. glaberrima, and 58 RWR representing 21 species, for tolerance to Fe toxicity. Plants were grown in a semi-artificial greenhouse setup, in which they were exposed either to control conditions, an Fe shock during the vegetative growth stage (acute treatment), or to a continuous moderately high Fe level (chronic treatment). In both stress treatments, foliar Fe concentrations were characteristic of Fe toxicity, and plants developed foliar stress symptoms, which were more pronounced in the chronic Fe stress especially toward the end of the growing season. Among the genotypes that produced seeds, only the chronic stress treatment significantly reduced yields due to increases in spikelet sterility. Moreover, a moderate but non-significant increase in grain Fe concentrations, and a significant increase in grain Zn concentrations were seen in chronic stress. Both domesticated rice and RWR exhibited substantial genotypic variation in their responses to Fe toxicity. Although no RWR strikingly outperformed domesticated rice in Fe toxic conditions, some genotypes scored highly in individual traits. Two O. meridionalis accessions were best in avoiding foliar symptom formation in acute Fe stress, while an O. rufipogon accession produced the highest grain yields in both chronic and acute Fe stress. In conclusion, this study provides the basis for using interspecific crosses for adapting rice to Fe toxicity.

Current status of genomic resources on wild relatives of rice.

Rice is a food crop of global importance, cultivated in diverse agro-climatic zones of the world. However, in the process of domestication many beneficial alleles have been eroded from the gene pool of the rice cultivated globally and eventually has made it vulnerable to a plethora of stresses. In contrast, the wild relatives of rice, despite being agronomically inferior, have inherited a potential of surviving in a range of geographical habitats. These adaptations enrich them with novel traits that upon introgression to modern cultivated varieties offer tremendous potential of increasing yield and adaptability. But, due to the unavailability of their genetic as well as genomic resources, identification and characterisation of these novel beneficial alleles has been a challenging task. Nevertheless, with the unprecedented surge in the area of conservation genomics, researchers have now shifted their focus towards these natural repositories of beneficial traits. Presently, there are several generic and specialized databases harboring genome-wide information on wild species of rice, and are acting as a useful resource for identification of novel genes and alleles, designing of molecular markers, comparative analysis and evolutionary biology studies. In this review, we introduce the key features of these databases focusing on their utility in rice breeding programs.

High resolution genetic mapping and identification of a candidate gene(s) for the purple sheath color and plant height in an interspecific F2 population derived from Oryza nivara Sharma & Shastry × Oryza sativa L. cross

Wild relatives of rice (Oryza sativa L.) represent enormous genetic diversity for many traits. Many domestication related traits found only in wild species that are lost from cultivated species during domestication. In this study, we report high-resolution mapping of two domestications related quantitative trait locus (QTL) controlling purple sheath color and plant height using high-density SNP based linkage map in an interspecific F2 population derived from a cross between O. nivara Sharma & Shastry and O. sativa. The segregation ratio of purple sheath color fit into 3:1 indicated that the presence of a dominant gene. The segregation of plant height trait exhibited a normal distribution in F2 and F2:3 generations. QTL analysis showed the identification of two QTLs controlling purple sheath color (designated as qPsh6.1 and qPsh6.2) on chromosome 6 explaining 27.12% and 14% phenotypic variance, respectively. The only plant height QTL (tentatively designated as qPh1.9) was mapped on chromosome 1 contributing 18.3% phenotypic variance. The qPsh6.1 covers 25.17 Kb region flanked by AX-95928721 and AX-95954573 containing five open reading frames (ORFs) while qPsh6.2 spanned in 118.2 Kb region containing 19 ORFs flanked by markers AX-95956260 and AX-95928295. The qPh1.9 gene controlling plant height was mapped between two SNP markers, AX-95944819 and AX-95964796 co-segregated with the locus LOC_Os01g66690 encoding for ZIP4/SPO22 protein. The detailed genetic study of the location of these genes will be useful for the map-based cloning.

Two SNP Mutations Turned off Seed Shattering in Rice.

Seed shattering is an important agronomic trait in rice domestication. In this study, using a near-isogenic line (NIL-hs1) from Oryza barthii, we found a hybrid seed shattering phenomenon between the NIL-hs1 and its recurrent parent, a japonica variety Yundao 1. The heterozygotes at hybrid shattering 1 (HS1) exhibited the shattering phenotype, whereas the homozygotes from both parents conferred the non-shattering. The causal HS1 gene for hybrid shattering was located in the region between SSR marker RM17604 and RM8220 on chromosome 4. Sequence verification indicated that HS1 was identical to SH4, and HS1 controlled the hybrid shattering due to harboring the ancestral haplotype, the G allele at G237T site and C allele at C760T site from each parent. Comparative analysis at SH4 showed that all the accessions containing ancestral haplotype, including 78 wild relatives of rice and 8 African cultivated rice, had the shattering phenotype, whereas all the accessions with either of the homozygous domestic haplotypes at one of the two sites, including 17 wild relatives of rice, 111 African cultivated rice and 65 Asian cultivated rice, showed the non-shattering phenotype. Dominant complementation of the G allele at G237T site and the C allele at C760T site in HS1 led to a hybrid shattering phenotype. These results help to shed light on the nature of seed shattering in rice during domestication and improve the moderate shattering varieties adapted to mechanized harvest.

Segregation Distortion Observed in the Progeny of Crosses Between Oryza sativa and O. meridionalis Caused by Abortion During Seed Development.

Wild rice relatives having the same AA genome as domesticated rice (Oryza sativa) comprise the primary gene pool for rice genetic improvement. Among them, O. meridionalis and O. rufipogon are found in the northern part of Australia. Three Australian wild rice strains, Jpn1 (O. rufipogon), Jpn2, and W1297 (O. meridionalis), and one cultivated rice cultivar Taichung 65 (T65) were used in this study. A recurrent backcrossing strategy was adopted to produce chromosomal segment substitution lines (CSSLs) carrying chromosomal segments from wild relatives and used for trait evaluation and genetic analysis. The segregation of the DNA marker RM136 locus on chromosome 6 was found to be highly distorted, and a recessive lethal gene causing abortion at the seed developmental stage was shown to be located between two DNA markers, KGC6_10.09 and KGC6_22.19 on chromosome 6 of W1297. We name this gene as SEED DEVELOPMENT 1 (gene symbol: SDV1). O. sativa is thought to share the functional dominant allele Sdv1-s (s for sativa), and O. meridionalis is thought to share the recessive abortive allele sdv1-m (m for meridionalis). Though carrying the sdv1-m allele, the O. meridionalis accessions can self-fertilize and bear seeds. We speculate that the SDV1 gene may have been duplicated before the divergence between O. meridionalis and the other AA genome Oryza species, and that O. meridionalis has lost the function of the SDV1 gene and has kept the function of another putative gene named SDV2.

Salt-Treated Roots of Oryza australiensis Seedlings are Enriched with Proteins Involved in Energetics and Transport.

Salinity is a major constraint on rice productivity worldwide. However, mechanisms of salt tolerance in wild rice relatives are unknown. Root microsomal proteins are extracted from two Oryza australiensis accessions contrasting in salt tolerance. Whole roots of 2-week-old seedlings are treated with 80mM NaCl for 30 days to induce salt stress. Proteins are quantified by tandem mass tags (TMT) and triple-stage Mass Spectrometry. More than 200 differentially expressed proteins between the salt-treated and control samples in the two accessions (p-value <0.05) are found. Gene Ontology (GO) analysis shows that proteins categorized as "metabolic process," "transport," and "transmembrane transporter" are highly responsive to salt treatment. In particular, mitochondrial ATPases and SNARE proteins are more abundant in roots of the salt-tolerant accession and responded strongly when roots are exposed to salinity. mRNA quantification validated the elevated protein abundances of a monosaccharide transporter and an antiporter observed in the salt-tolerant genotype. The importance of the upregulated monosaccharide transporter and a VAMP-like protein by measuring salinity responses of two yeast knockout mutants for genes homologous to those encoding these proteins in rice are confirmed. Potential new mechanisms of salt tolerance in rice, with implications for breeding of elite cultivars are also discussed.

Isolation and characterization of genes related to sheath blight resistance via the tagging of mutants in rice

Sheath blight disease (ShB) in rice is caused by Rhizoctonia solani. However, there have been no major genes identified from wild rice relatives and cultivated rice that encode resistance to R. solani. In this study, 300 Ds tagging mutants were generated via tissue culture regeneration methods from a Ds (dissociation) insertion line, and R. solani AG1-IA was inoculated to isolate the resistant mutants. The starter line that was homozygous (Ds-s) with a single Ds insertion in chromosome 1 exhibited a similar response to ShB as the non-transgenic plants. A Southern blot analysis showed that the Ds element was actively transposed in 300 R1 lines generated from Ds-s, and R2 plants were generated by selfing using 300 R1 lines with Ds insertions. Out of 300 R2 lines, two lines displayed susceptibility, and two lines exhibited strong resistance to ShB. In addition, 23 mutant lines displayed resistant symptoms, and the remaining 273 lines showed no differences compared to the ShB-susceptible wild-type control plants. Further examination revealed that the Ds gene was inserted at the second intron of either the PHYTOCHROME B (PHYB) or LAZY1 gene in two strong resistant mutants. We showed that the ethylene signaling genes (EIL1, EIL2, EIN2, and ERF63), jasmonic acid synthesis gene (LOX2), and salicylic acid signaling gene PBZ1 were up-regulated in the phyB mutants compared with the wild-type control that is susceptible to ShB. Further genetic study using EIL1 RNAi and EIL1 overexpression plants revealed that EIL1 positively regulates the resistance of rice to ShB. Overall, our analyses provided a basis for the identification of ShB resistance genes and the realization that PHYB negatively regulates the resistance of rice to ShB via the suppression of ethylene signaling.

Setting conservation priorities for the wild relatives of food crops in Indonesia

Crop wild relatives (CWR) have been increasingly used as a genetic resource in crop improvement programs, thus, their conservation is essential for future sustainable agriculture and food security. Generally, CWR are threatened but their conservation has just recently come to global attention. Ex situ conservation (to ensure the availability of material to plant breeders and reintroduction programs) and in situ conservation (to permit their natural evolution) need better planning to ensure success. However, Indonesia as one of the important areas for CWR diversity does not yet have specific plans to conserve these resources. The basis for CWR conservation planning is having a prioritized inventory of CWR upon which to focus CWR conservation actions in Indonesia. Therefore, the initial CWR conservation planning steps reported in this paper are CWR checklist development and subsequent prioritization to permit better allocation of resources and time for conservation action. A total of 1968 taxa were recorded as wild relatives of food crops in Indonesia. About 571 (29%) of those taxa are national endemics and 864 (44%) are narrow regional endemics. After prioritization based on the socio-economic value of the related crops and potential utilization for plant breeding, 234 taxa were established as a priority for conservation. Ninety-five of these priority taxa are important at the national and global levels (such as wild relatives of rice, banana, mango, breadfruit, sugarcane, taro, coconut, sweet potato, melon, sorghum, citrus, and aubergine), 69 are important at the national and regional levels (such as wild relatives of tropical fruits and sugar crops), and 70 taxa are important at global level only (such as wild relatives of yam, figs, and raspberry). Those priority taxa are now the target for further CWR conservation action both of ex situ and in situ gap analyses and the establishment of a systematic conservation planning strategy for effective conservation action in Indonesia.

Novel biotic stress responsive candidate gene based SSR (cgSSR) markers from rice

Developing host resistance is an effective measure to minimize the yield losses caused by biotic stresses in crop plants. Generation of genomic resources greatly facilitates the development of resistant plants. Microsatellite markers speed up the selection procedure and introgression of resistant alleles in rice breeding programme. Candidate gene based SSR (cgSSR) markers are preferred over genomic SSR due to their tighter linkage with the trait governing loci. This study describes the identification and analysis of cgSSR markers from biotic stress responsive genes of rice. Among the selected 308 different biotic stress responsive genes of rice, 176 gene sequences were found to harbour a total of 364 SSR loci. Tri-nucleotide motif was found to be the most abundant (51.09%), followed by di- (45.05%) and tetra-nucleotide (3.84%). Intron and CDS are the two locations where most of the cgSSR loci were found, followed by 5′UTR and 3′UTR. In order to validate, polymorphism survey was done in 25 Oryza sativa genotypes using 35 cgSSR primer pairs. Among the 35 cgSSR, 27 cgSSR exhibited loci specific amplification with an average allele number of 5.66 per primer and mean PIC value of 0.226. Further, out of 27, 21 cgSSRs were found to be cross transferable to the wild species belonging to the Sativa complex; while 19 were found to be transferable to the species belonging to the Officinalis complex. The novel biotic stress-responsive cgSSR markers developed here could be used in marker-assisted introgression and pyramiding of resistant allele into elite rice cultivars from other rice germplasm as well as from wild relatives of rice.

Status of Rice (Oryza sativa L.) Genepool Collected from Western Ghats Region of India: Gap Analysis and Diversity Distribution Mapping using GIS Tools

This paper analyses the genetic resources of cultivated and wild rice in Western Ghats region (WGR) spread in six states of the country. Landraces and wild relatives of rice (Oryza sativa L.) always form a priority germplasm for exploration, collections, conservation, evaluation and utilization. Western Ghats region is one of the 35 biodiversity hot-spots of the world and harbour large diversity of rice under its varied climatic and edaphic conditions. So far, ICAR-NBPGR, New Delhi has collected 2, 758 accessions of cultivated and 49 of wild rice germplasm from 42 districts of WGR of India. Germplasm collecting sites linked with geo-coordinates forms geo-referenced map which showed that Kerala had significant representation (2, 036 accessions), followed by Karnataka (203), Maharashtra (201), Tamil Nadu (153), Gujarat (116) and Goa (49). Highest numbers of landraces were collected from Kerala (386), followed by Tamil Nadu (92), Karnataka (88), Gujarat (56), Goa (30) and Maharashtra (26). GIS-based grid map shows that highest numbers of landraces were collected from north and central regions of Kerala, validated by the highest Shannon-Weaver diversity index (2.1–2.8). Diverse agro-ecosystems as well as selection by farmers for various uses and traits, coupled with extensive exploration efforts might have lead to the assemblage of such landraces collection from Kerala. Collected wild rice germplasm consists six taxa -Oryza meyeriana var. granulata (11), O. nivara (4), O. officinalis (4), O. rufipogon (10), O. sativa f. spontanea (19) and O. officinalis subsp. malampuzhaensis (1). Literature analysis revealed that, out of 678 rice landraces of this region, 43 have been identified/used in crop improvement as source of important traits viz. early and late maturity, aroma, high iron content, medicinal value, drought/cold/salt tolerance, resistance to brown plant hopper, etc. This analysis identified gaps and priority areas for future explorations.

Major Domestication-Related Phenotypes in Indica Rice Are Due to Loss of miRNA-Mediated Laccase Silencing.

Domestication of rice (Oryza sativa) included conversion of perennial wild species with few seeds to short plants that produced abundant seeds. Most domestication-associated changes were due to variations in transcription factors and other key proteins such as enzymes. Here, we show that multiple yield-related traits associated with indica rice domestication are linked to micro (mi) RNA-mediated regulation. Analysis of small (s) RNA data sets from cultivated indica rice lines, a few landraces, and two wild relatives of rice revealed the presence of abundant 22-nucleotide (nt) reads in wild relatives that mapped to miR397 precursors. miR397 was expressed at very high levels in wild relatives and at negligible levels in high-yielding cultivated lines. In its genera-specific form of 22-nt, miR397 targeted mRNAs encoding laccases that decayed and induced robust secondary cascade silencing in wild species that required RNA-dependent RNA polymerase 6. In wild species of rice, reduced expression of laccases resulted in low lignification. As expected, overexpression of miR397 induced de-domestication phenotypes. At least 26 uncharacterized QTLs previously implicated in rice yield overlapped with laccases and miR397 genes. These results suggest that miRNAs contribute to rice domestication-associated phenotypes.

Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.

This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF versions of the article.