New Genetic Insights into Pearl Millet Diversity As Revealed by Characterization of Early- and Late-Flowering Landraces from Senegal

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food and a drought-tolerant cereal well adapted to Sub-Saharan Africa agro-ecosystems. An important diversity of pearl millet landraces has been widely conserved by farmers and therefore could help copping with climate changes and contribute to future food security. Hence, characterizing its genetic diversity and population structure can contribute to better assist breeding programs for a sustainable agricultural productivity enhancement. Toward this goal, a comprehensive panel of 404 accessions were used that correspond to 12 improved varieties, 306 early flowering and 86 late-flowering cultivated landraces from Senegal. Twelve highly polymorphic SSR markers were used to study diversity and population structure. Two genes, PgMADS11 and PgPHYC, were genotyped to assess their association to flowering phenotypic difference in landraces. Results indicate a large diversity and untapped potential of Senegalese pearl millet germplasm as well as a genetic differentiation between early- and late-flowering landraces. Further, a fine-scale genetic difference of PgPHYC and PgMADS11 (SNP and indel, respectively) and co-variation of their alleles with flowering time were found among landraces. These findings highlight new genetic insights of pearl millet useful to define heterotic populations for breeding, genomic association panel, or crosses for trait-specific mapping

Genome scan reveals selection acting on genes linked to stress response in wild pearl millet

Uncovering genomic regions involved in adaption is a major goal in evolutionary biology. High-throughput sequencing now makes it possible to tackle this challenge in nonmodel species. Yet, despite the increasing number of methods targeted to specifically detect genomic footprints of selection, the complex demography of natural populations often causes high rates of false positive in gene discoveries. The aim of this study was to identify climate adaptations in wild pearl millet populations, Cenchrus americanus ssp. monodii. We focused on two climate gradients, one in Mali and one in Niger. We used a two-step strategy to limit false-positive outliers. First, we considered gradients as biological replicates and performed RNA sequencing of four populations at the extremities. We combined four methods-three based on differentiation among populations and one based on diversity patterns within populations-to identify outlier SNPs from a set of 87 218 high-quality SNPs. Among 11 155 contigs of pearl millet reference transcriptome, 540 exhibited selection signals as evidenced by at least one of the four methods. In a second step, we genotyped 762 samples in 11 additional populations distributed along the gradients using SNPs from the detected contigs and random SNPs as control. We further assessed selection on this large data set using a differentiation-based method and a method based on correlations with environmental variables based. Four contigs displayed consistent signatures between the four extreme and 11 additional populations, two of which were linked to abiotic and biotic stress responses

Genetic Characterization of Taiwan Commercial Native Chickens Ascertained by Microsatellite Markers

Taiwan commercial native chickens have played a vital role in the domestic market due to Taiwanese traditional cooking style and culture. This study investigated the genetic characterization and population structure of 10 Taiwan commercial native chicken populations, together with two exotic breeds and one population of red jungle fowl, using 22 microsatellites. The results showed that Taiwan commercial native chickens generally harbored high genetic diversity but lower than that of red jungle fowl population in terms of number of alleles and gene diversity. The neighbor-joining tree revealed a poor resolution with only two branches showing bootstrap values above 70%. Based on Bayesian clustering approach, thirteen populations were inferred into eight distinct clusters namely Game bird, B strain, L2 strain, White Broiler and White Leghorn with an average proportion of membership higher than 0.90 and the values higher than 0.85 for red jungle fowl, Hakim chicken and Hakka strain while four remaining breeds were closely related together. The population structure showed Taiwan commercial native chickens are more admixed, in contrast to occidental highly productive breeds. The high genetic variation within breed as shown in the results of the analysis of molecular variance, facilitated by gene exchanges, did not allow discriminating in an efficient way. This suggests that the genetic pool of Taiwan commercial native chickens is well distributed among breeds and therefore there is a good potential for adaptation to new environmental conditions or markets. Some populations, namely L2 strain and B strain showed very high inbreeding coefficient and thus could be considered at risks. Therefore, management needs to be taken into account for the populations, to prevent inbreeding depression and maintain genetic diversity

New Genetic Insights into Pearl Millet Diversity As Revealed by Characterization of Early- and Late-Flowering Landraces from Senegal

International audiencePearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food and a drought-tolerant cereal well adapted to Sub-Saharan Africa agro-ecosystems. An important diversity of pearl millet landraces has been widely conserved by farmers and therefore could help copping with climate changes and contribute to future food security. Hence, characterizing its genetic diversity and population structure can contribute to better assist breeding programs for a sustainable agricultural productivity enhancement. Toward this goal, a comprehensive panel of 404 accessions were used that correspond to 12 improved varieties, 306 early flowering and 86 late-flowering cultivated landraces from Senegal. Twelve highly polymorphic SSR markers were used to study diversity and population structure. Two genes, PgMADS11 and PgPHYC, were genotyped to assess their association to flowering phenotypic difference in landraces. Results indicate a large diversity and untapped potential of Senegalese pearl millet germplasm as well as a genetic differentiation between early-and late-flowering landraces. Further, a fine-scale genetic difference of PgPHYC and PgMADS11 (SNP and indel, respectively) and co-variation of their alleles with flowering time were found among landraces. These findings highlight new genetic insights of pearl millet useful to define heterotic populations for breeding, genomic association panel, or crosses for trait-specific mapping

Myosin XI is associated with fitness and adaptation to aridity in wild pearl millet

International audiencePhenotypic changes in plants can be observed along many environmental gradients and are determined by both environmental and genetic factors. The identification of alleles associated with phenotypic variations is a rapidly developing area of research.We studied the genetic basis of phenotypic variations in 11 populations of wild pearl millet (Pennisetum glaucum) on two NorthSouth aridity gradients, one in Niger and one in Mali. Most of the 11 phenotypic traits assessed in a common garden experimentvaried between the populations studied. Moreover, the size of the inflorescence, the number of flowers and aboveground dry mass co-varied positively with a decrease in rainfall. To decipher the genetic basis of these phenotypes, we used an associationmapping strategy with a mixed model. We found two SNPs on the same myosin XI contig significantly associated with variations in the average number of flowers. Both the allele frequency of the two SNPs and the average number of flowers co-varied withthe rainfall gradient on the two gradients. Interestingly, this gene was also a target of selection during domestication. The Myosin XI gene is thus a good candidate for fitness-related adaptation in wild populations

Séquençage du génome entier et diversité génétique de populations sauvages et domestiques de pintade

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Genomic footprints of selection in early-and late-flowering pearl millet landraces

Pearl millet is among the top three-cereal production in one of the most climate vulnerable regions, sub-Saharan Africa. Its Sahelian origin makes it adapted to grow in poor sandy soils under low soil water regimes. Pearl millet is thus considered today as one of the most interesting crops to face the global warming. Flowering time, a trait highly correlated with latitude, is one of the key traits that could be modulated to face future global changes. West African pearl millet landraces, can be grouped into early- (EF) and late-flowering (LF) varieties, each flowering group playing a specific role in the functioning and resilience of Sahelian smallholders. The aim of this study was thus to detect genes linked to flowering but also linked to relevant traits within each flowering group. We thus investigated genomic and phenotypic diversity in 109 pearl millet landrace accessions, i.e., 66 early-flowering and 43 late-flowering, grown in the groundnut basin, the first area of rainfed agriculture in Senegal dominated by dry cereals (millet, maize, and sorghum) and legumes (groundnuts, cowpeas). We were able to confirm the role of PhyC gene in pearl millet flowering and identify several other genes that appear to be as much as important, such as FSR12 and HAC1. HAC1 and two other genes appear to be part of QTLs previously identified and deserve further investigation. At the same time, we were able to highlight a several genes and variants that could contribute to the improvement of pearl millet yield, especially since their impact was demonstrated across flowering cycles

CARACTERISATION PHENOTYPIQUE ET GENETIQUE DU RIZ AFRICAIN (ORYZA GLABERRIMA STEUD) PHENOTYPIC AND GENETIC CHARACTERIZATION OF AFRICAN RICE (ORYZA GLABERRIMA STEUD).

<p>The agronomic interest of African rice and the morphological similarities with other species, arouse the necessity to characterize African rice for recovery and conservation. The present study aims primarily to characterize phenotypically and genetically African rice for better exploitation in aid of rice producers and consumers. Indeed, the phenotypic characteristics of the rice accessions examined have been determined in two agronomics systems (upland and irrigated) carried out about 235 accessions of African rice; and afterwards, genetic characterization using a specific marker has been carried. At the end of the analyzes, with regard to the phenotypic characters, 22 O.sativa or interspecific accessions differing morphologically on several descriptors were identified. Genetically, out of 19 profiles revealed on a 935-bp band, 14 confirmed the phenotypic results. This study shows that 221 out of 235 accessions are O. glaberrima rice. These results show that the accessions of different species analyzed were confused during the collection. They also seems to validate the possibility of hybridization between the two rice species in peasant environment. The accessions characterized strengthen the conservation effort of African rice. This collection can be used for future studies, particularly with perspective to selection and running African rice with the possibility to establish a genetic model to facilitate the transfer of useful genes from O.glaberrima to O.sativa, while controlling the reproductive barrier. Thus, it will be easy to better exploit the genetic diversity of the African species of cultivated rice.</p