Glutaredoxin regulation of primary root growth is associated with early drought stress tolerance in pearl millet.

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet's early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modeling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including genome-wide association study and quantitative trait loci (QTL) approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re-annotation of one of these genomic regions identified a glutaredoxin-encoding gene PgGRXC9 as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homolog AtROXY19 revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment.

Pearl millet is a staple food for over 90 million people living in regions of Africa and India that typically experience high temperatures and little rainfall. It was domesticated about 4,500 years ago in the Sahel region of West Africa and is one of the most heat and drought tolerant cereal crops worldwide. In most plants, organs known as roots absorb water and essential nutrients from the soil. Young pearl millet plants develop a fast-growing primary root, but it is unclear how this unique feature helps the crop to grow in hot and dry conditions. Using weather data collected from the Sahel over a 20-year period, Fuente, Grondin et al. predicted by modelling that early drought stress is the major factor limiting pearl millet growth and yield in this region. Field experiments found that plants with primary roots that grow faster within soil were better at tolerating early drought than those with slower growing roots. Further work using genetic approaches revealed that a gene known as PgGRXC9 promotes the growth of the primary root. To better understand how this gene works, the team examined a very similar gene in a well-studied model plant known as Arabidopsis. This suggested that PgGRXC9 helps the primary root to grow by stimulating cell elongation within the root. Since it is well adapted to dry conditions, pearl millet is expected to play an important role in helping agriculture adjust to climate change. The findings of Fuente, Grondin et al. may be used by plant breeders to create more resilient and productive varieties of pearl millet.

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.

Maximizing value of genetic sequence data requires an enabling environment and urgency.

Severe price spikes of the major grain commodities and rapid expansion of cultivated area in the past two decades are symptoms of a severely stressed global food supply. Scientific discovery and improved agricultural productivity are needed and are enabled by unencumbered access to, and use of, genetic sequence data. In the same way the world witnessed rapid development of vaccines for COVID-19, genetic sequence data afford enormous opportunities to improve crop production. In addition to an enabling regulatory environment that allowed for the sharing of genetic sequence data, robust funding fostered the rapid development of coronavirus diagnostics and COVID-19 vaccines. A similar level of commitment, collaboration, and cooperation is needed for agriculture.

Transcriptomic analysis of methyl jasmonate treatment reveals gene networks involved in drought tolerance in pearl millet.

Water deficit stress at the early stage of development is one of the main factors limiting pearl millet production. One practice to counteract this limitation would be to resort to the application of hormones to stimulate plant growth and development at critical stages. Exogenous methyl jasmonate (MeJA) can improve drought tolerance by modulating signaling, metabolism, and photosynthesis pathways, therefore, we assumed that can occur in pearl millet during the early stage of development. To decipher the molecular mechanisms controlling these pathways, RNAseq was conducted in two pearl millet genotypes, drought-sensitive SosatC88 and drought-tolerant Souna3, in response to 200 µM of MeJA. Pairwise comparison between the MeJA-treated and non-treated plants revealed 3270 differentially expressed genes (DEGs) among 20,783 transcripts in SosatC88 and 127 DEGs out of 20,496 transcripts in Souna3. Gene ontology (GO) classification assigned most regulated DEGs in SosatC88 to heme binding, oxidation-reduction process, response to oxidative stress and membrane, and in Souna3 to terpene synthase activity, lyase activity, magnesium ion binding, and thylakoid. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis reveals that DEGs in SosatC88 are related to the oxidation-reduction process, the biosynthesis of other secondary metabolites, the signal transduction, and the metabolism of terpenoids, while in Souna3, DEGs are related to the metabolism of terpenoids and the energy metabolism. Two genes encoding a diterpenoid biosynthesis-related (Pgl_GLEAN_10009413) and a Glutathione S transferase T3 (Pgl_GLEAN_10034098) were contra-regulated between SosatC88 and Souna3. Additionally, five random genes differentially expressed by RNAseq were validated using qPCR, therefore, they are potential targets for the development of novel strategies breeding schemes for plant growth under water deficit stress. These insights into the molecular mechanisms of pearl millet genotype tolerance at the early stage of development contribute to the understanding of the role of hormones in adaptation to drought-prone environments.

GWAS unveils features between early- and late-flowering pearl millets.

BACKGROUND: Pearl millet, a nutritious food for around 100 million people in Africa and India, displays extensive genetic diversity and a high degree of admixture with wild relatives. Two major morphotypes can be distinguished in Senegal: early-flowering Souna and late-flowering Sanio. Phenotypic variabilities related to flowering time play an important role in the adaptation of pearl millet to climate variability. A better understanding of the genetic makeup of these variabilities would make it possible to breed pearl millet to suit regions with different climates. The aim of this study was to characterize the genetic basis of these phenotypic differences. RESULTS: We defined a core collection that captures most of the diversity of cultivated pearl millets in Senegal and includes 60 early-flowering Souna and 31 late-flowering Sanio morphotypes. Sixteen agro-morphological traits were evaluated in the panel in the 2016 and 2017 rainy seasons. Phenological and phenotypic traits related with yield, flowering time, and biomass helped differentiate early- and late-flowering morphotypes. Further, using genotyping-by-sequencing (GBS), 21,663 single nucleotide polymorphisms (SNPs) markers with more than 5% of minor allele frequencies were discovered. Sparse non-negative matrix factorization (sNMF) analysis confirmed the genetic structure in two gene pools associated with differences in flowering time. Two chromosomal regions on linkage groups (LG 3) (~ 89.7 Mb) and (LG 6) (~ 68.1 Mb) differentiated two clusters among the early-flowering Souna. A genome-wide association study (GWAS) was used to link phenotypic variation to the SNPs, and 18 genes were linked to flowering time, plant height, tillering, and biomass (P-value < 2.3E-06). CONCLUSIONS: The diversity of early- and late-flowering pearl millet morphotypes in Senegal was captured using a heuristic approach. Key phenological and phenotypic traits, SNPs, and candidate genes underlying flowering time, tillering, biomass yield and plant height of pearl millet were identified. Chromosome rearrangements in LG3 and LG6 were inferred as a source of variation in early-flowering morphotypes. Using candidate genes underlying these features between pearl millet morphotypes will be of paramount importance in breeding for resilience to climatic variability.

Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration.

Climate change is already affecting agro-ecosystems and threatening food security by reducing crop productivity and increasing harvest uncertainty. Mobilizing crop diversity could be an efficient way to mitigate its impact. We test this hypothesis in pearl millet, a nutritious staple cereal cultivated in arid and low-fertility soils in sub-Saharan Africa. We analyze the genomic diversity of 173 landraces collected in West Africa together with an extensive climate dataset composed of metrics of agronomic importance. Mapping the pearl millet genomic vulnerability at the 2050 horizon based on the current genomic-climate relationships, we identify the northern edge of the current areas of cultivation of both early and late flowering varieties as being the most vulnerable to climate change. We predict that the most vulnerable areas will benefit from using landraces that already grow in equivalent climate conditions today. However, such seed-exchange scenarios will require long distance and trans-frontier assisted migrations. Leveraging genetic diversity as a climate mitigation strategy in West Africa will thus require regional collaboration.

Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties.

BACKGROUND: Genetic improvement of pearl millet is lagging behind most of the major crops. Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutritional quality. Genotyping a breeding population with high throughput markers enables exploration of genetic diversity, population structure, and linkage disequilibrium (LD) which are important preludes for marker-trait association studies and application of genomic-assisted breeding. RESULTS: Genotyping-by-sequencing (GBS) libraries of 309 inbred lines derived from landraces and improved varieties from Africa and India generated 54,770 high quality single nucleotide polymorphism (SNP) markers. On average one SNP per 29 Kb was mapped in the reference genome, with the telomeric regions more densely mapped than the pericentromeric regions of the chromosomes. Population structure analysis using 30,208 SNPs evenly distributed in the genome divided 309 accessions into five subpopulations with different levels of admixture. Pairwise genetic distance (GD) between accessions varied from 0.09 to 0.33 with the average distance of 0.28. Rapid LD decay implied low tendency of markers inherited together. Genetic differentiation estimates were the highest between subgroups 4 and 5, and the lowest between subgroups 1 and 2. CONCLUSIONS: Population genomic analysis of pearl millet inbred lines derived from diverse geographic and agroecological features identified five subgroups mostly following pedigree differences with different levels of admixture. It also revealed the prevalence of high genetic diversity in pearl millet, which is very useful in defining heterotic groups for hybrid breeding, trait mapping, and holds promise for improving pearl millet for yield and nutritional quality. The short LD decay observed suggests an absence of persistent haplotype blocks in pearl millet. The diverse genetic background of these lines and their low LD make this set of germplasm useful for traits mapping.

Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut.

A deep understanding of the genetic control of drought tolerance and iron deficiency tolerance is essential to hasten the process of developing improved varieties with higher tolerance through genomics-assisted breeding. In this context, an improved genetic map with 1205 loci was developed spanning 2598.3 cM with an average 2.2 cM distance between loci in the recombinant inbred line (TAG 24 × ICGV 86031) population using high-density 58K single nucleotide polymorphism (SNP) "Axiom_Arachis" array. Quantitative trait locus (QTL) analysis was performed using extensive phenotyping data generated for 20 drought tolerance- and two iron deficiency tolerance-related traits from eight seasons (2004-2015) at two locations in India, one in Niger, and one in Senegal. The genome-wide QTL discovery analysis identified 19 major main-effect QTLs with 10.0-33.9% phenotypic variation explained (PVE) for drought tolerance- and iron deficiency tolerance- related traits. Major main-effect QTLs were detected for haulm weight (20.1% PVE), SCMR (soil plant analytical development (SPAD) chlorophyll meter reading, 22.4% PVE), and visual chlorosis rate (33.9% PVE). Several important candidate genes encoding glycosyl hydrolases; malate dehydrogenases; microtubule-associated proteins; and transcription factors such as MADS-box, basic helix-loop-helix (bHLH), NAM, ATAF, and CUC (NAC), and myeloblastosis (MYB) were identified underlying these QTL regions. The putative function of these genes indicated their possible involvement in plant growth, development of seed and pod, and photosynthesis under drought or iron deficiency conditions in groundnut. These genomic regions and candidate genes, after validation, may be useful to develop molecular markers for deploying genomics-assisted breeding for enhancing groundnut yield under drought stress and iron-deficient soil conditions.

Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation.

Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as "adaptive introgression". Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers' knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.

Response to early drought stress and identification of QTLs controlling biomass production under drought in pearl millet.

Pearl millet plays a major role in food security in arid and semi-arid areas of Africa and India. However, it lags behind the other cereal crops in terms of genetic improvement. The recent sequencing of its genome opens the way to the use of modern genomic tools for breeding. Our study aimed at identifying genetic components involved in early drought stress tolerance as a first step toward the development of improved pearl millet varieties or hybrids. A panel of 188 inbred lines from West Africa was phenotyped under early drought stress and well-irrigated conditions. We found a strong impact of drought stress on yield components. This impact was variable between inbred lines. We then performed an association analysis with a total of 392,493 SNPs identified using Genotyping-by-Sequencing (GBS). Correcting for genetic relatedness, genome wide association study identified QTLs for biomass production in early drought stress conditions and for stay-green trait. In particular, genes involved in the sirohaem and wax biosynthesis pathways were found to co-locate with two of these QTLs. Our results might contribute to breed pearl millet lines with improved yield under drought stress.

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments.

Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

Genome-wide analysis of cytosine DNA methylation revealed salicylic acid promotes defense pathways over seedling development in pearl millet.

Cytosine DNA methylation is an epigenetic regulatory system used by plants to control gene expression. Methylation pattern always changes after abiotic stresses, pathogens and pest infections or after a treatment with salicylic acid (SA). The latter is a key player in plant development and defense against insect herbivores, pathogens, and abiotic stresses. The roles of SA on the methylation patterns and the plant development were performed in 4 pearl millet (Pennisetum glaucum) varieties. Seedlings of 4 early-flowering photosensitive genotypes (PMS3, PMI8, PMG, and PMT2) were grown on MS medium supplemented with null or different doses of SA. Root growth was used as a parameter to evaluate the effects of SA at early stage development. DNA from these seedlings was extracted and Methylation-Sensitive Amplified Polymorphism (MSAP) was measured to assess the effects of SA on methylome. The methylation analysis revealed that SA treatment decreased the methylation, while inhibiting the root growth for all varieties tested, except in PMG at 0.5 mM, indicating a dose and a genotype response-dependence. The methylation level was positively correlated with the root growth. This suggests that SA influences both the methylome by demethylation activities and the root growth by interfering with the root development-responsive genes. The demethylation process, induced by the REPRESSOR OF SILCENCING 1 (ROS1) may activate R genes, or GH3.5 and downregulate the hormonal pathway under root development. These findings showed the pearl millet metabolism prioritized and promoted the defense pathways over vegetative development during stress.

Pearl Millet Genetic Traits Shape Rhizobacterial Diversity and Modulate Rhizosphere Aggregation.

Root exudation contributes to soil carbon allocation and also to microbial C and energy supply, which subsequently impacts soil aggregation around roots. Biologically-driven soil structural formation is an important driver of soil fertility. Plant genetic determinants of exudation and more generally of factors promoting rhizosphere soil aggregation are largely unknown. Here, we characterized rhizosphere aggregation in a panel of 86 pearl millet inbred lines using a ratio of root-adhering soil dry mass per root tissue dry mass (RAS/RT). This ratio showed significant variations between lines, with a roughly 2-fold amplitude between lowest and highest average values. For 9 lines with contrasting aggregation properties, we then compared the bacterial diversity and composition in root-adhering soil. Bacterial α-diversity metrics increased with the "RAS/RT ratio." Regarding taxonomic composition, the Rhizobiales were stimulated in lines showing high aggregation level whereas Bacillales were more abundant in lines with low ratio. 184 strains of cultivable exopolysaccharides-producing bacteria have been isolated from the rhizosphere of some lines, including members from Rhizobiales and Bacillales. However, at this stage, we could not find a correlation between abundance of EPS-producing species in bacterial communities and the ratio RAS/RT. These results illustrated the impact of cereals genetic trait variation on soil physical properties and microbial diversity. This opens the possibility of considering plant breeding to help management of soil carbon content and physical characteristics through carbon rhizodeposition in soil.

Structure of sweet potato (Ipomoea batatas) diversity in West Africa covaries with a climatic gradient.

Sub-Saharan agriculture has been identified as vulnerable to ongoing climate change. Adaptation of agriculture has been suggested as a way to maintain productivity. Better knowledge of intra-specific diversity of varieties is prerequisites for the successful management of such adaptation. Among crops, root and tubers play important roles in food security and economic growth for the most vulnerable populations in Africa. Here, we focus on the sweet potato. The Sweet potato (Ipomoea batatas) was domesticated in Central and South America and was later introduced into Africa and is now cultivated throughout tropical Africa. We evaluated its diversity in West Africa by sampling a region extending from the coastal area of Togo to the northern Sahelian region of Senegal that represents a range of climatic conditions. Using 12 microsatellite markers, we evaluated 132 varieties along this gradient. Phenotypic data from field trials conducted in three seasons was also obtained. Genetic diversity in West Africa was found to be 18% lower than in America. Genetic diversity in West Africa is structured into five groups, with some groups found in very specific climatic areas, e.g. under a tropical humid climate, or under a Sahelian climate. We also observed genetic groups that occur in a wider range of climates. The genetic groups were also associated with morphological differentiation, mainly the shape of the leaves and the color of the stem or root. This particular structure of diversity along a climatic gradient with association to phenotypic variability can be used for conservation strategies. If such structure is proved to be associated with specific climatic adaptation, it will also allow developing strategies to adapt agriculture to ongoing climate variation in West Africa.

TaVRT2 represses transcription of the wheat vernalization gene TaVRN1.

In wheat, VRN1/TaVRN1 and VRN2/TaVRN2 determine the growth habit and flowering time. In addition, the MADS box transcription factor VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (TaVRT2) is also associated with the vernalization response in a manner similar to TaVRN2. However, the molecular relationship between these three genes and their products is unknown. Using transient expression assays in Nicotiana benthamiana, we show that TaVRT2 acts as a repressor of TaVRN1 transcription. TaVRT2 binds the CArG motif in the TaVRN1 promoter and represses its activity in vivo. In contrast, TaVRN2 does not bind the TaVRN1 promoter and has no direct effect on its activity, but it can enhance the repression effect of TaVRT2. This suggests that a repressor complex regulates the expression of TaVRN1. In winter wheat, TaVRT2, TaVRN2 and TaVRN1 transcripts accumulate in the shoot apical meristem and young leaves, and temporal expression is consistent with TaVRT2 and TaVRN2 being repressors of floral transition, whereas TaVRN1 is an activator. Non-vernalized spring wheat grown under a short-day photoperiod accumulates TaVRT2 and shows a delay in flowering, suggesting that TaVRT2 is regulated independently by photoperiod and low temperature. The data presented suggest that TaVRT2, in association with TaVRN2, represses the transcription of TaVRN1.