Sophie Bouchet

A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers.

BackgroundSorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers.ResultsThe six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a Neighbours approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci (1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions.ConclusionThe final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available.

Massive Sorghum Collection Genotyped with SSR Markers to Enhance Use of Global Genetic Resources

Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated. Except for Kafir, there was little correspondence between races and marker-based groups. Bicolor, Caudatum, Durra and Guinea types were each dispersed in three groups or more. Races should therefore better be referred to as morphotypes. Wild and weedy accessions were very diverse and scattered among cultivated samples, reinforcing the idea that large gene-flow exists between the different compartments. Our study provides an entry to global sorghum germplasm collections. Our reference marker kit can serve to aggregate additional studies and enhance international collaboration. We propose a core reference set in order to facilitate integrated phenotyping experiments towards refined functional understanding of sorghum diversity.

Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild–weedy–crop complex in a western African region

Gene flow between domesticated plants and their wild relatives is one of the major evolutionary processes acting to shape their structure of genetic diversity. Earlier literature, in the 1970s, reported on the interfertility and the sympatry of wild, weedy and cultivated sorghum belonging to the species Sorghum bicolor in most regions of sub-Saharan Africa. However, only a few recent surveys have addressed the geographical and ecological distribution of sorghum wild relatives and their genetic structure. These features are poorly documented, especially in western Africa, a centre of diversity for this crop. We report here on an exhaustive in situ collection of wild, weedy and cultivated sorghum assembled in Mali and in Guinea. The extent and pattern of genetic diversity were assessed with 15 SSRs within the cultivated pool (455 accessions), the wild pool (91 wild and weedy forms) and between them. FST and RST statistics, distance-based trees, Bayesian clustering methods, as well as isolation by distance models, were used to infer evolutionary relationships within the wild–weedy–crop complex. Firstly, our analyses highlighted a strong racial structure of genetic diversity within cultivated sorghum (FSTxa0=xa00.40). Secondly, clustering analyses highlighted the introgressed nature of most of the wild and weedy sorghum and grouped them into two eco-geographical groups. Such closeness between wild and crop sorghum could be the result of both sorghum’s domestication history and preferential post-domestication crop-to-wild gene flow enhanced by farmers’ practices. Finally, isolation by distance analyses showed strong spatial genetic structure within each pool, due to spatially limited dispersal, and suggested consequent gene flow between the wild and the crop pools, also supported by RST analyses. Our findings thus revealed important features for the collection, conservation and biosafety of domesticated and wild sorghum in their centre of diversity.

Genetic diversity of taro (Colocasia esculenta (L.) Schott) in Vanuatu (Oceania): an appraisal of the distribution of allelic diversity (DAD) with SSR markers

In Vanuatu, an oceanic archipelago located in south-west Pacific, taro (Colocasia esculenta (L.) Schott) is one of the staple crops. An eco-geographical survey of its genetic resources was conducted in ten villages, each located on a different island. A sample of 344 landraces referred as the National Sample (NS) was collected. Its genetic diversity was assessed using nine microsatellites markers and then was compared with an International Core Sample (ICS) that was previously distributed in the ten villages of the study in order to test the geographical distribution of allelic diversity as an effective mean for the on-farm conservation of root crops. The ICS was composed of 41 accessions, including 23 originating from South-East Asia. The molecular dataset revealed in the NS (1) 324 distinct multilocus genotypes, (2) six genetic clusters mainly differentiated by rare alleles, (3) a geographical structure of the genetic resources of taro based, within each village, on the dominance of one or two of these clusters rather that their exclusivity, and (4) an analogy between the patterns of dominant clusters between villages and the past and present social networks. In addition, accessions from the ICS revealed 52 new alleles. Based on these findings, we formulate hypotheses regarding the processes involved in the genetic diversification of taro in Vanuatu. We also discuss the use of this set of microsatellite markers along with the molecular dataset obtained from this study as effective tools to monitor the diversity and evolution of taro in the future.

Flowering Time in Maize: Linkage and Epistasis at a Major Effect Locus

In a previous study, we identified a candidate fragment length polymorphism associated with flowering time variation after seven generations of selection for flowering time, starting from the maize inbred line F252. Here, we characterized the candidate region and identified underlying polymorphisms. Then, we combined QTL mapping, association mapping, and developmental characterization to dissect the genetic mechanisms responsible for the phenotypic variation. The candidate region contained the Eukaryotic Initiation Factor (eIF-4A) and revealed a high level of sequence and structural variation beyond the 3′-UTR of eIF-4A, including several insertions of truncated transposable elements. Using a biallelic single-nucleotide polymorphism (SNP) (C/T) in the candidate region, we confirmed its association with flowering time variation in a panel of 317 maize inbred lines. However, while the T allele was correlated with late flowering time within the F252 genetic background, it was correlated with early flowering time in the association panel with pervasive interactions between allelic variation and the genetic background, pointing to underlying epistasis. We also detected pleiotropic effects of the candidate polymorphism on various traits including flowering time, plant height, and leaf number. Finally, we were able to break down the correlation between flowering time and leaf number in the progeny of a heterozygote (C/T) within the F252 background consistent with causal loci in linkage disequilibrium. We therefore propose that both a cluster of tightly linked genes and epistasis contribute to the phenotypic variation for flowering time.

Dent and Flint maize diversity panels reveal important genetic potential for increasing biomass production

AbstractKey messageGenetic and phenotypic analysis of two complementary maize panels revealed an important variation for biomass yield. Flowering and biomass QTL were discovered by association mapping in both panels.AbstractnThe high whole plant biomass productivity of maize makes it a potential source of energy in animal feeding and biofuel production. The variability and the genetic determinism of traits related to biomass are poorly known. We analyzed two highly diverse panels of Dent and Flint lines representing complementary heterotic groups for Northern Europe. They were genotyped with the 50xa0k SNP-array and phenotyped as hybrids (crossed to a tester of the complementary pool) in a western European field trial network for traits related to flowering time, plant height, and biomass. The molecular information revealed to be a powerful tool for discovering different levels of structure and relatedness in both panels. This study revealed important variation and potential genetic progress for biomass production, even at constant precocity. Association mapping was run by combining genotypes and phenotypes in a mixed model with a random polygenic effect. This permitted the detection of significant associations, confirming height and flowering time quantitative trait loci (QTL) found in literature. Biomass yield QTL were detected in both panels but were unstable across the environments. Alternative kinship estimator only based on markers unlinked to the tested SNP increased the number of significant associations by around 40xa0% with a satisfying control of the false positive rate. This study gave insights into the variability and the genetic architectures of biomass-related traits in Flint and Dent lines and suggests important potential of these two pools for breeding high biomass yielding hybrid varieties.

Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces

BackgroundPearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal.ResultsWe identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (π), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage.ConclusionsWe identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops.

Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population

In crop species, adaptation to different agroclimatic regions creates useful variation but also leads to unwanted genetic correlations. Bouchet....... Adaptation of domesticated species to diverse agroclimatic regions has led to abundant trait diversity. However, the resulting population structure and genetic heterogeneity confounds association mapping of adaptive traits. To address this challenge in sorghum [Sorghum bicolor (L.) Moench]—a widely adapted cereal crop—we developed a nested association mapping (NAM) population using 10 diverse global lines crossed with an elite reference line RTx430. We characterized the population of 2214 recombinant inbred lines at 90,000 SNPs using genotyping-by-sequencing. The population captures ∼70% of known global SNP variation in sorghum, and 57,411 recombination events. Notably, recombination events were four- to fivefold enriched in coding sequences and 5′ untranslated regions of genes. To test the power of the NAM population for trait dissection, we conducted joint linkage mapping for two major adaptive traits, flowering time and plant height. We precisely mapped several known genes for these two traits, and identified several additional QTL. Considering all SNPs simultaneously, genetic variation accounted for 65% of flowering time variance and 75% of plant height variance. Further, we directly compared NAM to genome-wide association mapping (using panels of the same size) and found that flowering time and plant height QTL were more consistently identified with the NAM population. Finally, for simulated QTL under strong selection in diversity panels, the power of QTL detection was up to three times greater for NAM vs. association mapping with a diverse panel. These findings validate the NAM resource for trait mapping in sorghum, and demonstrate the value of NAM for dissection of adaptive traits.

Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits

Plant architecture, phenology and yield components of cultivated plants have repeatedly been shaped by selection to meet human needs and adaptation to different environments. Here we assessed the genetic architecture of 24 correlated maize traits that interact during plant cycle. Overall, 336 lines were phenotyped in a network of 9 trials and genotyped with 50K single-nucleotide polymorphisms. Phenology was the main factor of differentiation between genetic groups. Then yield components distinguished dents from lower yielding genetic groups. However, most of trait variation occurred within group and we observed similar overall and within group correlations, suggesting a major effect of pleiotropy and/or linkage. We found 34 quantitative trait loci (QTLs) for individual traits and six for trait combinations corresponding to PCA coordinates. Among them, only five were pleiotropic. We found a cluster of QTLs in a 5u2009Mb region around Tb1 associated with tiller number, ear row number and the first PCA axis, the latter being positively correlated to flowering time and negatively correlated to yield. Kn1 and ZmNIP1 were candidate genes for tillering, ZCN8 for leaf number and Rubisco Activase 1 for kernel weight. Experimental repeatabilities, numbers of QTLs and proportion of explained variation were higher for traits related to plant development such as tillering, leaf number and flowering time, than for traits affected by growth such as yield components. This suggests a simpler genetic determinism with larger individual QTL effects for the first category.

Population genomics of sorghum (Sorghum bicolor) across diverse agroclimatic zones of Niger

Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed 516 Nigerien accessions for which local variety name, botanical race, and geographic origin were known. We discovered 144u2009299 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). We performed discriminant analysis of principal components (DAPC), which identified six genetic groups, and performed a genome scan for loci with high discriminant loadings. The highest discriminant coefficients were on chromosome 9, near the putative ortholog of maize flowering time adaptation gene Vgt1. Next, we characterized differentiation among local varieties and used a genome scan of pairwise FST values to identify SNPs associated with specific local varieties. Comparison of varieties named for light- versus dark-grain identified differentiation near Tannin1, the major gene responsible for grain tannins. These findings could facilitate genomics-assisted breeding of locally adapted and farmer-preferred sorghum varieties for Niger.