Genome-wide association studies using 50 K rice genic SNP chip unveil genetic architecture for anaerobic germination of deep-water rice population of Assam, India.

North Eastern part of India such as Assam is inundated by flood every year where the farmers are forced to grow the traditional tall deep-water rice. Genetic improvement of this type of rice is slow because of insufficient knowledge about their genetic architecture and population structure. In the present investigation, the genetic diversity architecture of 94 deep-water rice genotypes of Assam and association mapping strategy was, for the first time, applied to determine the significant SNPs and genes for deep-water rice. These genotypes are known for their unique elongation ability under deep-water condition. The anaerobic germination (AG) related trait-associated genes identified here can provide affluent resources for rice breeding especially in flood-prone areas. We investigated the genome-wide association studies (GWAS) using 50 K rice genic SNP chip across 94 deep-water rice genotypes collected from different flood-prone districts/villages of Assam. Population structure and diversity analysis revealed that these genotypes were stratified into four sub-populations. Using GWAS approach, 20 significant genes were identified and found to be associated with AG-related traits. Of them, two most relevant genes (OsXDH1and SSXT) have been identified which explain phenotypic variability (R2 > 20%) in the population. These genes were located in Chr 3 (LOC_Os03g31550) which encodes for enzyme xanthine dehydrogenase 1(OsXDH1) and in Chr 12 (LOC_Os12g31350) which encodes for SSXT family protein. Both of these genes were found to be associated with anaerobic response index (increase in the coleoptile length under water in anaerobic condition with respect to control), respectively. Interestingly, OsXDH1is involved in purine catabolism pathway and acts as a scavenger of reactive oxygen species in plants, whereas SSXT is GRF1-interacting factor 3. These two candidate genes associated with AG of deep-water rice have been found to be reported for the first time. Thus, this study provides a greater resource for breeders not only for improvement of deep-water rice, but also for AG tolerant variety useful for direct-seeded rice in flood-affected areas.

Understanding natural genetic variation for nutritional quality in grain and identification of superior haplotypes in deepwater rice genotypes of Assam, India.

Rice grown under deepwater ecosystem is considered to be natural farming and hence they are considered to be input efficient. Thus, to identify gene responsible for nutritional content under natural conditions, a genome-wide association study (GWAS)was performed. GWAS identified single nucleotide polymorphisms (SNPs) significantly associated with various nutritional quality traits such as Zn (mg/kg), Fe (mg/kg), Protein (%), Oil (%), Amylose (%), Starch (%), Phytic acid (%), Phenol (%) and TDF (%) in 184 deepwater rice accessions evaluated over 2 consecutive years. A total of 278 SNPs distributed across 12 chromosomes were found to be significantly associated with Zn, Oil and Phenol content. Among them, eight high confidence SNPs were significant and identified on chr1 (AX-95933712), chr7 (AX-95957036), and chr8 (AX-95965181) for Zn content. Similarly, on chr2 (AX-95945186), chr8 (AX-95964718), and chr11 (AX-95961099) have been found to be associated with Oil content and on chr3 (AX-95922121) and chr4 (AX-95963889) for Phenol content. Genomic regions of ± 220 kb flanking the three consistent lowest p value containing SNPs for each trait were considered for finding superior haplotypes. These SNPs showed significant phenotypic variations with different identified haplotype blocks. The allelic variations with phenotypes were considered to be superior haplotypes i.e., Block 1: Hap 1 (ACCC) for high Zn content, Block 2: Hap 1 (CT) for high Oil content, and Block 2: Hap 1(CGGG) for low Phenol content. The discovered superior haplotype with high nutritional content could be important for understanding the mechanisms involving nutrient use efficiency. Thus, the present study demonstrated that developing rice varieties with appropriate nutritional quality traits will be possible through the incorporation of such superior haplotypes in breeding programs.

Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis).

Marker-assisted breeding and tagging of important quantitative trait loci for beneficial traits are two important strategies for the genetic improvement of plants. However, the scarcity of diverse and informative genetic markers covering the entire tea genome limits our ability to achieve such goals. In the present study, we used a comparative genomic approach to mine the tea genomes of Camellia sinensis var. assamica (CSA) and C. sinensis var. sinensis (CSS) to identify the markers to differentiate tea genotypes. In our study, 43 and 60 Camellia sinensis miniature inverted-repeat transposable element (CsMITE) families were identified in these two sequenced tea genomes, with 23,170 and 37,958 putative CsMITE sequences, respectively. In addition, we identified 4912 non-redundant, Camellia sinensis intron length polymorphic (CsILP) markers, 85.8% of which were shared by both the CSS and CSA genomes. To validate, a subset of randomly chosen 10 CsMITE markers and 15 CsILP markers were tested and found to be polymorphic among the 36 highly diverse tea genotypes. These genome-wide markers, which were identified for the first time in tea plants, will be a valuable resource for genetic diversity analysis as well as marker-assisted breeding of tea genotypes for quality improvement.

TeaMiD: a comprehensive database of simple sequence repeat markers of tea.

Tea is a highly cross-pollinated, woody, perennial tree. High heterozygosity combined with a long gestational period makes conventional breeding a cumbersome process. Therefore, marker-assisted breeding is a better alternative approach when compared with conventional breeding. Considering the large genome size of tea (~3 Gb), information about simple sequence repeat (SSR) is scanty. Thus, we have taken advantage of the recently published tea genomes to identify large numbers of SSR markers in the tea. Besides the genomic sequences, we identified SSRs from the other publicly available sequences such as RNA-seq, GSS, ESTs and organelle genomes (chloroplasts and mitochondrial) and also searched published literature to catalog validated set of tea SSR markers. The complete exercise yielded a total of 935 547 SSRs. Out of the total, 82 SSRs were selected for validation among a diverse set of tea genotypes. Six primers (each with four to six alleles, an average of five alleles per locus) out of the total 27 polymorphic primers were used for a diversity analysis in 36 tea genotypes with mean polymorphic information content of 0.61-0.76. Finally, using all the information generated in this study, we have developed a user-friendly database (TeaMiD; http://indianteagenome.in:8080/teamid/) that hosts SSR from all the six resources including three nuclear genomes of tea and transcriptome sequences of 17 Camellia wild species. Database URL: http://indianteagenome.in:8080/teamid/.