Natural crossing in rice

et al. 2023

Rice

Analyses of the genetic bases of plant adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 and 2011) of the autogamous crop species, Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1 °C on average) and rainfall regime (less predictable and reduced amount) in the target areas. Second, phenotyping the populations for phenology, we observed significantly earlier heading time in the 2010 samples. Third, implementing two genome-scan methods (one of which specially developed for selfing species) on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of them bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results illustrate the evolution of in situ diversity through processes of human and natural selection, and provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetic models for adaptation of plant populations to environmental changes. To our best knowledge, this is the first study dealing with climate-changes’ selective footprint in crops.

Section: Discussionmentioning

confidence: 99%

Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes’ Selective Footprints in the Genes Network Regulating Flowering Time

et al. 2023

Rice

“…In our case, while the occurrence of adaptive mutations cannot be excluded, their spread to a significant share of the O. sativa and O. glaberrima subpopulations is unlikely given the length of generation in rice (one year), the rather short interval (31 years) separating our two collect times and the rather low rate of outcrossing in rice. Indeed, the highest natural outcrossing rate reported is 6.8% in O. sativa (Sahadevan & Namboodiri, 1963) and 5% in O. glaberrima (Oka & Morishima, 1967). Analysing the distribution of rice genetic diversity at farm, village and ecosystem levels in Guinea, using SSR molecular markers, Barry et al (2007b; 2007c) reported that (i) rice landraces had a multi-line genetic structure; (ii) the within- and between-farm F ST values were of the same order of magnitude; (iii) within-farm genetic diversity was high, i.e., up to 50% of total genetic diversity observed at the village level; (iv) each village pooled more than half of the regional allelic diversity; (v) regional allelic diversity was comparable to that noted worldwide for the Asian rice (O. sativa), but not as high for the African rice ( O. glaberrima ).…”

Section: Discussionmentioning

confidence: 99%

Genome scan of landrace populations of the self-fertilizing crop species rice, collected across time, revealed climate changes’ selective footprints in the genes network regulating flowering time

et al. 2022

Preprint

Analysis of the genetic bases of adaptation to climate changes are often conducted on natural populations. We report here on a study based on diachronic sampling (1980 & 2010) of the self-fertilising crop species, Oryza sativa (Asian rice) and Oryza glaberrima (African rice), in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+1°C on average) and rainfall regime (less predictable and reduced amount) in the target area. Second, phenotyping the populations for phenology, we observed significantly earlier heading time (up to 10 days) in the 2010 samples. Third, we implemented two genome-scan methods, one of which specially developed for selfing species, and detected 31 independent selection footprints. These loci showed significant enrichment in genes involved in reproductive processes and bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. We argue that this high adaptive potential results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds well before the advent of the environmental selective pressure. The complex selection footprints observed in this empirical study calls for further model development on genetic bases of plant adaptation to environmental changes.

“…In our case, while the occurrence of adaptive mutations cannot be excluded, their spread to a signi cant share of the O. sativa and O. glaberrima subpopulations is unlikely given the length of generation in rice (one year), the rather short interval (31 years) separating our two collect times and the rather low rate of outcrossing in rice. Indeed, the highest natural outcrossing rate reported is 6.8% in O. sativa (Sahadevan & Namboodiri, 1963) and 5% in O. glaberrima (Oka & Morishima, 1967). Analysing the distribution of rice genetic diversity at farm, village and ecosystem levels in Guinea, using SSR molecular markers, Barry et al (2007b;2007c) reported that (i) rice landraces had a multi-line genetic structure; (ii) the within-and between-farm F ST values were of the same order of magnitude; (iii) within-farm genetic diversity was high, i.e., up to 50% of total genetic diversity observed at the village level; (iv) each village pooled more than half of the regional allelic diversity; (v) regional allelic diversity was comparable to that noted worldwide for the Asian rice (O. sativa), but not as high for the African rice (O. glaberrima).…”

Section: Discussionmentioning

confidence: 99%

Genome scan of rice landrace populations collected across time revealed climate changes’ selective footprints in the genes network regulating flowering time

et al. 2022

Preprint

Analysis of the genetic bases of plants adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 & 2010) of the autogamous crop species, Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1°C on average) and rainfall regime (less predictable and reduced amount) in the target area. Second, phenotyping the populations for phenology, we observed significantly earlier heading time (up to 10 days) in the 2010 samples. Third, implementing two genome-scan methods (one of which specially developed for selfing species) on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of theme bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetics models for adaptation of plants populations to environmental changes.