BIOSTATISTICS APPLICATIONS FOR TROPICAL (AND NON) PLANT AND ANIMAL BIOLOGY: A (META)GENOMICS PERSPECTIVE

Next-generation sequencing and high-throughput SNP-genotyping have wide applications in plant and animal genomics and metagenomics. Such applications provide insights into population genetics and are used to develop tools to assist agriculture. In rice, through GWAS the SD-1 gene allele linked to semi-dwarf phenotype was found to be still segregating in temperate japonica accessions, while in indica and tropical japonica accessions was either absent (wild type) or fixed (semi-dwarf lines). With a similar approach, SNP associated with yield have been identified in rice accessions under limited-water conditions: the identified associations are suitable targets for genomics-assisted breeding to improve yield-related traits under limited water conditions. In sugar beet, alleles for genetic resistance to diseases are typically introduced through introgression from wild beets. By sequencing 21 resistance genes for rhizomania and nematode infections, wild and cultivated beets did indeed cluster together, except one gene: this last reveals a resistance mutation that originated directly in domestic beets. With metagenomics, significant differences have been observed in the gut microbiota composition of BALBc mice (animal model for Graves' thyroid disease) immunized with the same protocol in comparable specific-pathogen free units from different centers. These differences help explain the lack of reproducibility of the animal model across centres. Similarly, the gut microbiota may be implicated in genotype-by-environment interactions found in livestock when farming the same breed in different places (e.g. temperate vs tropical latitudes). In cattle, the rumen microbiome has a major role in methane production, a green- house gas implicated in global climate change. Feed supplementation modulate the rumen microbiota composition, and specifically reduce the counts of methanogenic taxa. These results can be applied to farming and breeding for reduced methane emissions in cattle.