Abstract
Understanding crops genetic diversity and the evolutionary processes that accompanied their world-wide spread is useful for designing effective breeding strategies. Madagascar Island was one of the last major Old World areas where human settlement was accompanied by the introduction of Oryza sativa. Early studies had reported the presence in the island of a rice group specific to Madagascar. Using 24K SNP, we compared diversity patterns at the whole genome and at haplotypes (30 SNP-long segments along the genome) levels, between 620 Malagasy and 1,929 Asian rice accessions. The haplotypes level analysis aimed at identifying local genotypic variations, relative to the whole genome level, using a group assignment method that relies on kernel density estimation in a Principal Component Analysis feature space. Migration bottleneck had resulted in 10–25% reduction of diversity among the Malagasy representatives of indica (G1) and japonica (G6) populations. Compared to their Asian counterpart, G1 and G6 showed slightly lower indica and japonica introgressions, suggesting the latter population had undergone less recombinations when migration to the island occurred. The origins of G1 and G6 was delineated to XI-2 indica subpopulation from the Indian subcontinent and to tropical japonica from the Malay Archipelago, respectively. The Malagasy-specific group (Gm) had a rather high gene diversity and an original haplotype pattern: much lower share of indica haplotypes, and much higher share of Aus and japonica haplotypes than G1 and indica. Its emergence and expansion are most probably due to inter-group recombination facilitated by sympatry between indica-cAus admixes and “Bulu” type landraces of G6 in the highlands of Madagascar, and to human selection for adaptation to the lowland ecosystems of the highlands. Pattern of rice genetic diversity was also tightly associated with the history of human settlement in the island. Emergence of the Gm group is associated with the latest arrivals of Austronesians, who founded the Merina kingdom in the central highlands and developed lowland rice cultivation. As an intermediary form between Aus, indica and japonica, the three pillars of O. sativa domestication, Gm represents a very valuable genetic resource in breeding for adaptation to cold tolerance in tropical highlands.
Genetic Diversity of Campylobacter jejuni Isolates from Korea and Travel-Associated Cases from East and Southeast Asian Countries
