RESUMEN
On Madagascar, the illegal and unsustainable exploitation and illegal international trade of Dalbergia (rosewood) precious woods remain a serious conservation problem. Members of this genus are at high risk of extinction as a consequence of logging, mining, and slash and burn agriculture. Morphological identification of these Malagasy species is difficult in the absence of flowers and fruits, especially in the case of cut trees, sawn wood, and finished product. In this study, we use molecular barcoding to identify the Dalbergia species with the intent to contribute to the control of their illegal trade. Thirty-six Dalbergia samples representing 12 Malagasy species of which 11 have high commercial value, were collected to test the efficacy of a region of the plastid genome (rbcL) and a nuclear-transcribed ITS for barcoding. These widely used markers, as well as DNA barcoding gaps, "best match" and "best close match" approaches, and the neighbor-joining method were employed. All samples were amplified and sequenced using the two markers. Using a single locus, the "best match" and "best close match" approaches revealed that ITS has high discriminatory power within the tested Malagasy species. The combination of rbcL + ITS revealed 100% species discrimination. This study confirms that ITS alone and in combination with chloroplast barcode rbcL allow non-ambiguous identification for the 12 species studied. The results contribute to the development of DNA barcoding as a useful tool to identify Malagasy Dalbergia and suggest that the approach developed should be expanded to all 56 potentially exploited species in reference to international CITES requirements and the sustainable management of valuable resources.
RESUMEN
Understanding crops genetic diversity and the evolutionary processes that accompanied their worldwide spread is useful for designing effective breeding strategies. Madagascar Island was one of the last major Old World areas where human settlement brought the introduction of Oryza sativa. Early studies in the island had reported the presence of a rice group specific to Madagascar. Using 24 K SNP, we compared diversity patterns at the whole genome and at haplotype (30 SNP-long segments along the genome) levels, between 620 Malagasy and 1929 Asian rice accessions. The haplotype 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 and japonica populations. Compared to their Asian counterpart, they showed slightly lower indica and japonica introgressions, suggesting the two populations had undergone less recombination when migration to the island occurred. The origins of the Malagasy indica and japonica groups were delineated to 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 indica. Its emergence and expansion are most probably due to inter-group recombination facilitated by sympatry between indica-Aus admixes and "Bulu" type landraces of japonica in the central high plateaux of Madagascar, and to human selection for adaptation to the lowland rice cultivation. 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 high plateaux 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. We proposed the name Rojo for this new rice group.
