Identification of Candidate Genes Regulating Drought Tolerance in Pearl Millet.

Pearl millet is an important crop of the arid and semi-arid ecologies to sustain food and fodder production. The greater tolerance to drought stress attracts us to examine its cellular and molecular mechanisms via functional genomics approaches to augment the grain yield. Here, we studied the drought response of 48 inbreds representing four different maturity groups at the flowering stage. A set of 74 drought-responsive genes were separated into five major phylogenic groups belonging to eight functional groups, namely ABA signaling, hormone signaling, ion and osmotic homeostasis, TF-mediated regulation, molecular adaptation, signal transduction, physiological adaptation, detoxification, which were comprehensively studied. Among the conserved motifs of the drought-responsive genes, the protein kinases and MYB domain proteins were the most conserved ones. Comparative in-silico analysis of the drought genes across millet crops showed foxtail millet had most orthologs with pearl millet. Of 698 haplotypes identified across millet crops, MyC2 and Myb4 had maximum haplotypes. The protein-protein interaction network identified ABI2, P5CS, CDPK, DREB, MYB, and CYP707A3 as major hub genes. The expression assay showed the presence of common as well as unique drought-responsive genes across maturity groups. Drought tolerant genotypes in respective maturity groups were identified from the expression pattern of genes. Among several gene families, ABA signaling, TFs, and signaling proteins were the prospective contributors to drought tolerance across maturity groups. The functionally validated genes could be used as promising candidates in backcross breeding, genomic selection, and gene-editing schemes in pearl millet and other millet crops to increase the yield in drought-prone arid and semi-arid ecologies.

Deciphering the antagonistic effect of Streptomyces spp. and host-plant resistance induction against charcoal rot of sorghum.

MAIN CONCLUSION: The findings of this study suggest that the selected five strains of Streptomyces spp. could be used for biological control of charcoal rot disease in sorghum. Two strains each of Streptomyces albus (CAI-17 and KAI-27) and Streptomyces griseus (KAI-26 and MMA-32) and one strain of Streptomyces cavourensis (SAI-13) previously reported to have plant growth-promotion activity in chickpea, rice and sorghum were evaluated for their antagonistic potential against Macrophomina phaseolina, which causes charcoal rot in sorghum. The antagonistic potential of these strains against M. phaseolina was assessed through dual culture assay, metabolite production assay, blotter paper assay in greenhouse and field disease screens. In both dual culture and metabolite production assays, the selected strains significantly inhibited the growth of M. phaseolina (63-74%). In the blotter paper assay, all the five strains of Streptomyces spp. inhibited the pathogen (80-90%). When these five strains were tested for their antagonistic potential under the greenhouse (two times) and field (two seasons) conditions by toothpick method of inoculation, significant differences were observed for charcoal rot severity. Principal component analysis capturing 91.3% phenotypic variations, revealed that the shoot samples treated with both Streptomyces and the pathogen exhibited significantly enhanced antioxidant parameters including superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, glutathione reductase, phenylalanine ammonia-lyase, polyphenol oxidase, and total phenolic contents when compared to shoot samples treated with only M. phaseolina. Scanning electron microscope analysis revealed that the phloem and xylem tissues of the Streptomyces treated stem samples were intact compared to that of pathogen inoculated plants. This study indicated that the selected strains of Streptomyces spp. have the potential for biological control of charcoal rot disease in sorghum.

Drought and High Temperature Stress in Sorghum: Physiological, Genetic, and Molecular Insights and Breeding Approaches.

Sorghum is one of the staple crops for millions of people in Sub-Saharan Africa (SSA) and South Asia (SA). The future climate in these sorghum production regions is likely to have unexpected short or long episodes of drought and/or high temperature (HT), which can cause significant yield losses. Therefore, to achieve food and nutritional security, drought and HT stress tolerance ability in sorghum must be genetically improved. Drought tolerance mechanism, stay green, and grain yield under stress has been widely studied. However, novel traits associated with drought (restricted transpiration and root architecture) need to be explored and utilized in breeding. In sorghum, knowledge on the traits associated with HT tolerance is limited. Heat shock transcription factors, dehydrins, and genes associated with hormones such as auxin, ethylene, and abscisic acid and compatible solutes are involved in drought stress modulation. In contrast, our understanding of HT tolerance at the omic level is limited and needs attention. Breeding programs have exploited limited traits with narrow genetic and genomic resources to develop drought or heat tolerant lines. Reproductive stages of sorghum are relatively more sensitive to stress compared to vegetative stages. Therefore, breeding should incorporate appropriate pre-flowering and post-flowering tolerance in a broad genetic base population and in heterotic hybrid breeding pipelines. Currently, more than 240 QTLs are reported for drought tolerance-associated traits in sorghum prospecting discovery of trait markers. Identifying traits and better understanding of physiological and genetic mechanisms and quantification of genetic variability for these traits may enhance HT tolerance. Drought and HT tolerance can be improved by better understanding mechanisms associated with tolerance and screening large germplasm collections to identify tolerant lines and incorporation of those traits into elite breeding lines. Systems approaches help in identifying the best donors of tolerance to be incorporated in the SSA and SA sorghum breeding programs. Integrated breeding with use of high-throughput precision phenomics and genomics can deliver a range of drought and HT tolerant genotypes that can improve yield and resilience of sorghum under drought and HT stresses.

Biofortification to avoid malnutrition in humans in a changing climate: Enhancing micronutrient bioavailability in seed, tuber, and storage roots.

Malnutrition results in enormous socio-economic costs to the individual, their community, and the nation's economy. The evidence suggests an overall negative impact of climate change on the agricultural productivity and nutritional quality of food crops. Producing more food with better nutritional quality, which is feasible, should be prioritized in crop improvement programs. Biofortification refers to developing micronutrient -dense cultivars through crossbreeding or genetic engineering. This review provides updates on nutrient acquisition, transport, and storage in plant organs; the cross-talk between macro- and micronutrients transport and signaling; nutrient profiling and spatial and temporal distribution; the putative and functionally characterized genes/single-nucleotide polymorphisms associated with Fe, Zn, and ß-carotene; and global efforts to breed nutrient-dense crops and map adoption of such crops globally. This article also includes an overview on the bioavailability, bioaccessibility, and bioactivity of nutrients as well as the molecular basis of nutrient transport and absorption in human. Over 400 minerals (Fe, Zn) and provitamin A-rich cultivars have been released in the Global South. Approximately 4.6 million households currently cultivate Zn-rich rice and wheat, while ~3 million households in sub-Saharan Africa and Latin America benefit from Fe-rich beans, and 2.6 million people in sub-Saharan Africa and Brazil eat provitamin A-rich cassava. Furthermore, nutrient profiles can be improved through genetic engineering in an agronomically acceptable genetic background. The development of "Golden Rice" and provitamin A-rich dessert bananas and subsequent transfer of this trait into locally adapted cultivars are evident, with no significant change in nutritional profile, except for the trait incorporated. A greater understanding of nutrient transport and absorption may lead to the development of diet therapy for the betterment of human health.

Genetic and genomic interventions in crop biofortification: Examples in millets.

Micronutrient malnutrition is a serious threat to the developing world's human population, which largely relies on a cereal-based diet that lacks diversity and micronutrients. Besides major cereals, millets represent the key sources of energy, protein, vitamins, and minerals for people residing in the dryland tropics and drought-prone areas of South Asia and sub-Saharan Africa. Millets serve as multi-purpose crops with several salient traits including tolerance to abiotic stresses, adaptation to diverse agro-ecologies, higher productivity in nutrient-poor soils, and rich nutritional characteristics. Considering the potential of millets in empowering smallholder farmers, adapting to changing climate, and transforming agrifood systems, the year 2023 has been declared by the United Nations as the International Year of Millets. In this review, we highlight recent genetic and genomic innovations that can be explored to enhance grain micronutrient density in millets. We summarize the advances made in high-throughput phenotyping to accurately measure grain micronutrient content in cereals. We shed light on genetic diversity in millet germplasm collections existing globally that can be exploited for developing nutrient-dense and high-yielding varieties to address food and nutritional security. Furthermore, we describe the progress made in the fields of genomics, proteomics, metabolomics, and phenomics with an emphasis on enhancing the grain nutritional content for designing competitive biofortified varieties for the future. Considering the close genetic-relatedness within cereals, upcoming research should focus on identifying the genetic and genomic basis of nutritional traits in millets and introgressing them into major cereals through integrated omics approaches. Recent breakthroughs in the genome editing toolbox would be crucial for mainstreaming biofortification in millets.

Exploiting Indian landraces to develop biofortified grain sorghum with high protein and minerals.

Sorghum (Sorghum bicolor L. Moench) is the staple cereal and is the primary source of protein for millions of people in Asia and sub-Saharan Africa. Sorghum grain value has been increasing in tropical countries including India owing to its gluten-free nature, anti-oxidant properties and low glycemic index. However, the nutrient composition of modern cultivars is declining thus necessitating genetic biofortification of sorghum to combat malnutrition and improve nutritional balance in the human diet. Keeping this in view, efforts were made to utilize valuable alleles, associated with nutrient composition, that might have been left behind in the varietal development in sorghum. The study aimed to determine the genetic improvement for nine nutritional and quality parameters (crude protein, in vitro protein digestibility (IVPD), total iron (Fe), total zinc (Zn), bioavailable Fe (%), bioavailable Zn (%), total phenolics, tannins and antioxidant activity) in the grains of 19 sorghum genotypes (high yield, drought and grain mold tolerant) developed from 11 superior India's landraces. After selection and advancement made from 2017 to 2022 through single seed descent method, the improvement in the nine nutritional and quality parameters was assessed. Significant variation was observed for all the nine parameters among the landraces and the genotypes. Sorghum genotypes PYPS 2 and PYPS 13 recorded the highest crude protein (13.21 and 12.80% respectively) and IVPD (18.68 and 19.56% respectively). Majority of the sorghum genotypes recorded high Fe (14.21-28.41 mg/100 g) and Zn (4.81-8.16 mg/100 g). High phenolics and antioxidant activity were recorded in sorghum genotypes PYPS 18 (85.65 mg/g gallic acid equivalents) and PYPS 19 (89.78%) respectively. Selections through SSD method revealed highest improvement in genotype PYPS 10 for crude protein (32.25%), total phenolics (18.48%) and antioxidant activity (15.43%). High improvements in genotypes PYPS 12 (23.50%), PYPS 3 (26.79%), PYPS 15 (21.18%) were recorded for total Fe, available Fe and high tannins, respectively. The study demonstrated that landraces could be effectively utilized as a potential, low-cost and eco-friendly approach in sorghum genetic biofortification to improved sorghum productivity and nutritional supply in semi-arid tropics.

Rice biofortification: breeding and genomic approaches for genetic enhancement of grain zinc and iron contents.

Rice is a highly consumed staple cereal cultivated predominantly in Asian countries, which share 90% of global rice production. Rice is a primary calorie provider for more than 3.5 billion people across the world. Preference and consumption of polished rice have increased manifold, which resulted in the loss of inherent nutrition. The prevalence of micronutrient deficiencies (Zn and Fe) are major human health challenges in the 21st century. Biofortification of staples is a sustainable approach to alleviating malnutrition. Globally, significant progress has been made in rice for enhancing grain Zn, Fe, and protein. To date, 37 biofortified Fe, Zn, Protein and Provitamin A rich rice varieties are available for commercial cultivation (16 from India and 21 from the rest of the world; Fe > 10 mg/kg, Zn > 24 mg/kg, protein > 10% in polished rice as India target while Zn > 28 mg/kg in polished rice as international target). However, understanding the micronutrient genetics, mechanisms of uptake, translocation, and bioavailability are the prime areas that need to be strengthened. The successful development of these lines through integrated-genomic technologies can accelerate deployment and scaling in future breeding programs to address the key challenges of malnutrition and hidden hunger.

Combining ability studies of grain Fe and Zn contents of pearl millet (Pennisetum glaucum L.) in West Africa.

Micronutrient malnutrition is a major challenge in Africa, where half a million children die each year because of lack of micronutrients in their food. Pearl millet is an important food and fodder crop for the people living in the Semi-Arid regions of West Africa. The present study was conducted to determine the stability, combining ability, and gene action conditions of the high level of Fe and Zn content in grain and selected agronomic traits. Hence, eight genotypes were selected based on the availability of grain Fe and Zn contents and crossed in a full diallel mating design. Progenies from an 8 × 8 diallel mating along with the parents were evaluated in an alpha lattice design with three replications in three locations for two years. The parental lines Jirani, LCIC 9702 and MORO, had positive significant general combining ability (GCA) effects for grain Fe concentration, while Jirani and MORO had positive significant GCA effects for grain Zn concentration. For the specific combining ability (SCA), among the 56 hybrids evaluated, only the hybrids LCIC 9702 × Jirani and MORO × ZANGO had positive significant SCA effects for grain Fe concentration across locations, and for grain Zn concentration, the hybrids Gamoji × MORO, LCIC 9702 × Jirani, and ICMV 167006 × Jirani had positive significant SCA effects. The reciprocal effects were significant for grain Zn concentration, grain yield, flowering time, plant height, test weight, and downy mildew incidence, suggesting that the choice of a female or male parent is critical in hybrid production. Grain Fe and Zn concentration, flowering time, plant height, panicle length, panicle girth, panicle compactness, and downy mildew incidence were found to be predominantly under additive gene action, while grain yield and test weight were predominantly under non-additive gene action. A highly positive correlation was found between grain Fe and Zn concentrations, which implies that improving grain Fe trait automatically improves the grain Zn content. The stability analysis revealed that the hybrid ICMV 167006 × Jirani was the most stable and high-yielding with a high level of grain Fe and Zn micronutrients.

India's rainfed sorghum improvement: Three decades of genetic gain assessment for yield, grain quality, grain mold and shoot fly resistance.

Sorghum is a climate-resilient cereal and staple food crop for more than 200 million people in arid and semi-arid countries of Asia and Africa. Despite the economic importance, the productivity of sorghum in India is constrained by biotic and abiotic stresses such as incidences of shoot fly, grain mold and drought. Indian sorghum breeding focused on dual-purpose (grain and fodder), short-duration varieties with multiple resistance/tolerance to pests and diseases and improved nutritional quality (high protein, iron and zinc and low fat). In this context, it is important to ascertain the genetic progress made over 30 years by assessing the efficiency of past achievements in genetic yield potential and to facilitate future genetic improvement. The current study determined the genetic gain in 24 sorghum varieties developed by the national and state level research systems during 1990-2020. The 24 varieties were evaluated for three years (2018-2020) at six locations in Telangana state for yield, nutritional characteristics and tolerance to shoot fly and grain mold. The absolute grain yield genetic gain from the base year 1990 is 44.93 kg/ha/yr over the first released variety CSV 15. The realized mean yield increased from 2658 kg/ha of the variety CSV 15 in 1990s to 4069 kg/ha of SPV 2579 developed in 2020s. The absolute genetic gain for grain mold resistance is -0.11 per year with an overall relative gain of 1.46% over CSV 15. The top varieties for grain yield (SPV 2579, SPV 2678 and SPV 2578), fodder yield (PYPS 2, SPV 2769 and SPV 2679), shoot fly tolerance (PYPS 8, PYPS 2 and SPV 2179), mold tolerance (PYPS 8, PYPS 2 and SPV 2579) and high protein (PYPS 8, PYPS 2 and SPV 2769) were identified for possible scale up and further use in breeding program diversification. The study revealed that sorghum varieties bred with diverse genetic backgrounds such as landraces and with tolerance to pests and diseases had stable yield performance. Application of genomics and other precision tools can double genetic gains for these traits to strengthen sorghum cultivation in rainfed areas serving food and nutrition security.

Identification of iron and zinc responsive genes in pearl millet using genome-wide RNA-sequencing approach.

Pearl millet (Pennisetum glaucum L.), an important source of iron (Fe) and zinc (Zn) for millions of families in dryland tropics, helps in eradicating micronutrient malnutrition. The crop is rich in Fe and Zn, therefore, identification of the key genes operating the mineral pathways is an important step to accelerate the development of biofortified cultivars. In a first-of-its-kind experiment, leaf and root samples of a pearl millet inbred ICMB 1505 were exposed to combinations of Fe and Zn stress conditions using the hydroponics method, and a whole-genome transcriptome assay was carried out to characterize the differentially expressed genes (DEGs) and pathways. A total of 37,093 DEGs under different combinations of stress conditions were identified, of which, 7,023 and 9,996 DEGs were reported in the leaf and root stress treatments, respectively. Among the 10,194 unique DEGs, 8,605 were annotated to cellular, biological, and molecular functions and 458 DEGs were assigned to 39 pathways. The results revealed the expression of major genes related to the mugineic acid pathway, phytohormones, chlorophyll biosynthesis, photosynthesis, and carbohydrate metabolism during Fe and Zn stress. The cross-talks between the Fe and Zn provided information on their dual and opposite regulation of key uptake and transporter genes under Fe and Zn deficiency. SNP haplotypes in rice, maize, sorghum, and foxtail millet as well as in Arabidopsis using pearl millet Fe and Zn responsive genes could be used for designing the markers in staple crops. Our results will assist in developing Fe and Zn-efficient pearl millet varieties in biofortification breeding programs and precision delivery mechanisms to ameliorate malnutrition in South Asia and Sub-Saharan Africa.

Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding.

Pearl millet is a crucial nutrient-rich staple food in Asia and Africa and adapted to the climate of semi-arid topics. Since the genomic resources in pearl millet are very limited, we have developed a brand-new mid-density 4K SNP panel and demonstrated its utility in genetic studies. A set of 4K SNPs were mined from 925 whole-genome sequences through a comprehensive in-silico pipeline. Three hundred and seventy-three genetically diverse pearl millet inbreds were genotyped using the newly-developed 4K SNPs through the AgriSeq Targeted Genotyping by Sequencing technology. The 4K SNPs were uniformly distributed across the pearl millet genome and showed considerable polymorphism information content (0.23), genetic diversity (0.29), expected heterozygosity (0.29), and observed heterozygosity (0.03). The SNP panel successfully differentiated the accessions into two major groups, namely B and R lines, through genetic diversity, PCA, and structure models as per their pedigree. The linkage disequilibrium (LD) analysis showed Chr3 had higher LD regions while Chr1 and Chr2 had more low LD regions. The genetic divergence between the B- and R-line populations was 13%, and within the sub-population variability was 87%. In this experiment, we have mined 4K SNPs and optimized the genotyping protocol through AgriSeq technology for routine use, which is cost-effective, fast, and highly reproducible. The newly developed 4K mid-density SNP panel will be useful in genomics and molecular breeding experiments such as assessing the genetic diversity, trait mapping, backcross breeding, and genomic selection in pearl millet.

Breeding Drought-Tolerant Pearl Millet Using Conventional and Genomic Approaches: Achievements and Prospects.

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a C4 crop cultivated for its grain and stover in crop-livestock-based rain-fed farming systems of tropics and subtropics in the Indian subcontinent and sub-Saharan Africa. The intensity of drought is predicted to further exacerbate because of looming climate change, necessitating greater focus on pearl millet breeding for drought tolerance. The nature of drought in different target populations of pearl millet-growing environments (TPEs) is highly variable in its timing, intensity, and duration. Pearl millet response to drought in various growth stages has been studied comprehensively. Dissection of drought tolerance physiology and phenology has helped in understanding the yield formation process under drought conditions. The overall understanding of TPEs and differential sensitivity of various growth stages to water stress helped to identify target traits for manipulation through breeding for drought tolerance. Recent advancement in high-throughput phenotyping platforms has made it more realistic to screen large populations/germplasm for drought-adaptive traits. The role of adapted germplasm has been emphasized for drought breeding, as the measured performance under drought stress is largely an outcome of adaptation to stress environments. Hybridization of adapted landraces with selected elite genetic material has been stated to amalgamate adaptation and productivity. Substantial progress has been made in the development of genomic resources that have been used to explore genetic diversity, linkage mapping (QTLs), marker-trait association (MTA), and genomic selection (GS) in pearl millet. High-throughput genotyping (HTPG) platforms are now available at a low cost, offering enormous opportunities to apply markers assisted selection (MAS) in conventional breeding programs targeting drought tolerance. Next-generation sequencing (NGS) technology, micro-environmental modeling, and pearl millet whole genome re-sequence information covering circa 1,000 wild and cultivated accessions have helped to greater understand germplasm, genomes, candidate genes, and markers. Their application in molecular breeding would lead to the development of high-yielding and drought-tolerant pearl millet cultivars. This review examines how the strategic use of genetic resources, modern genomics, molecular biology, and shuttle breeding can further enhance the development and delivery of drought-tolerant cultivars.

Transition From Targeted Breeding to Mainstreaming of Biofortification Traits in Crop Improvement Programs.

Biofortification breeding for three important micronutrients for human health, namely, iron (Fe), zinc (Zn), and provitamin A (PVA), has gained momentum in recent years. HarvestPlus, along with its global consortium partners, enhances Fe, Zn, and PVA in staple crops. The strategic and applied research by HarvestPlus is driven by product-based impact pathway that integrates crop breeding, nutrition research, impact assessment, advocacy, and communication to implement country-specific crop delivery plans. Targeted breeding has resulted in 393 biofortified crop varieties by the end of 2020, which have been released or are in testing in 63 countries, potentially benefitting more than 48 million people. Nevertheless, to reach more than a billion people by 2030, future breeding lines that are being distributed by Consultative Group on International Agricultural Research (CGIAR) centers and submitted by National Agricultural Research System (NARS) to varietal release committees should be biofortified. It is envisaged that the mainstreaming of biofortification traits will be driven by high-throughput micronutrient phenotyping, genomic selection coupled with speed breeding for accelerating genetic gains. It is noteworthy that targeted breeding gradually leads to mainstreaming, as the latter capitalizes on the progress made in the former. Efficacy studies have revealed the nutritional significance of Fe, Zn, and PVA biofortified varieties over non-biofortified ones. Mainstreaming will ensure the integration of biofortified traits into competitive varieties and hybrids developed by private and public sectors. The mainstreaming strategy has just been initiated in select CGIAR centers, namely, International Maize and Wheat Improvement Center (CIMMYT), International Rice Research Institute (IRRI), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), International Institute of Tropical Agriculture (IITA), and International Center for Tropical Agriculture (CIAT). This review will present the key successes of targeted breeding and its relevance to the mainstreaming approaches to achieve scaling of biofortification to billions sustainably.

Association of Grain Iron and Zinc Content With Other Nutrients in Pearl Millet Germplasm, Breeding Lines, and Hybrids.

Micronutrient deficiency is most prevalent in developing regions of the world, including Africa and Southeast Asia where pearl millet (Pennisetum glaucum L.) is a major crop. Increasing essential minerals in pearl millet through biofortification could reduce malnutrition caused by deficiency. This study evaluated the extent of variability of micronutrients (Fe, Zn, Mn, and Na) and macronutrients (P, K, Ca, and Mg) and their relationship with Fe and Zn content in 14 trials involving pearl millet hybrids, inbreds, and germplasm. Significant genetic variability of macronutrients and micronutrients was found within and across the trials (Ca: 4.2-40.0 mg 100 g-1, Fe: 24-145 mg kg-1, Zn: 22-96 mg kg-1, and Na: 3.0-63 mg kg-1). Parental lines showed significantly larger variation for nutrients than hybrids, indicating their potential for use in hybrid parent improvement through recurrent selection. Fe and Zn contents were positively correlated and highly significant (r = 0.58-0.81; p < 0.01). Fe and Zn were positively and significantly correlated with Ca (r = 0.26-0.61; p < 0.05) and Mn (r = 0.24-0.50; p < 0.05). The findings indicate that joint selection for Fe, Zn, and Ca will be effective. Substantial genetic variation and high heritability (>0.60) for multiple grain minerals provide good selection accuracy prospects for genetic enhancement. A highly positive significant correlation between Fe and Zn and the nonsignificant correlation of grain macronutrients and micronutrients with Fe and Zn suggest that there is scope to achieve higher levels of Fe/Zn simultaneously in current pearl millet biofortification efforts without affecting other grain nutrients. Results suggest major prospects for improving multiple nutrients in pearl millet.

Addressing Iron and Zinc Micronutrient Malnutrition Through Nutrigenomics in Pearl Millet: Advances and Prospects.

Iron (Fe) and zinc (Zn) micronutrient deficiencies are significant health concerns, particularly among the underprivileged and resource-poor people in the semi-arid tropics globally. Pearl millet is regarded as a climate-smart crop with low water and energy footprints. It thrives well under adverse agro-ecologies such as high temperatures and limited rainfall. Pearl millet is regarded as a nutri-cereal owing to health-promoting traits such as high grain Fe and Zn content, metabolizable energy, high antioxidant and polyphenols, high proportion of slowly digestible starches, dietary fibers, and favorable essential amino acid profile compared to many cereals. Higher genetic variability for grain Fe and Zn content has facilitated considerable progress in mapping and mining QTLs, alleles and genes underlying micronutrient metabolism. This has been made possible by developing efficient genetic and genomic resources in pearl millet over the last decade. These include genetic stocks such as bi-parental RIL mapping populations, association mapping panels, chromosome segment substitution lines (CSSLs) and TILLING populations. On the genomics side, considerable progress has been made in generating genomic markers, such as SSR marker repository development. This was followed by the development of a next-generation sequencing-based genome-wide SNP repository. The circa 1,000 genomes re-sequencing project played a significant role. A high-quality reference genome was made available by re-sequencing of world diversity panel, mapping population parents and hybrid parental lines. This mini-review attempts to provide information on the current developments on mapping Fe and Zn content in pearl millet and future outlook.

Genetic Gains in Pearl Millet in India: Insights Into Historic Breeding Strategies and Future Perspective.

Pearl millet (Pennisetum glaucum R. Br.) is an important staple and nutritious food crop in the semiarid and arid ecologies of South Asia (SA) and Sub-Saharan Africa (SSA). In view of climate change, depleting water resources, and widespread malnutrition, there is a need to accelerate the rate of genetic gains in pearl millet productivity. This review discusses past strategies and future approaches to accelerate genetic gains to meet future demand. Pearl millet breeding in India has historically evolved very comprehensively from open-pollinated varieties development to hybrid breeding. Availability of stable cytoplasmic male sterility system with adequate restorers and strategic use of genetic resources from India and SSA laid the strong foundation of hybrid breeding. Genetic and cytoplasmic diversification of hybrid parental lines, periodic replacement of hybrids, and breeding disease-resistant and stress-tolerant cultivars have been areas of very high priority. As a result, an annual yield increase of 4% has been realized in the last three decades. There is considerable scope to further accelerate the efforts on hybrid breeding for drought-prone areas in SA and SSA. Heterotic grouping of hybrid parental lines is essential to sustain long-term genetic gains. Time is now ripe for mainstreaming of the nutritional traits improvement in pearl millet breeding programs. New opportunities are emerging to improve the efficiency and precision of breeding. Development and application of high-throughput genomic tools, speed breeding, and precision phenotyping protocols need to be intensified to exploit a huge wealth of native genetic variation available in pearl millet to accelerate the genetic gains.

Generation Mean Analysis Reveals the Predominant Gene Effects for Grain Iron and Zinc Contents in Pearl Millet.

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a climate-resilient dryland cereal that has been identified as a potential staple food crop that can contribute to alleviating micronutrient malnutrition, particularly with respect to grain iron (Fe) and zinc (Zn) contents, in Sub-Saharan Africa and India. In this regard, an understanding of the inheritance pattern of genes involved in Fe and Zn contents is vital for devising appropriate breeding methods to genetically enhance their levels in grains. In this study, we aimed to determine the genetic effects underlying such inheritance and their interactions based on the generation mean analyses. Four experimental crosses and their six generations (P1, P2, F1, BCP1, BCP2, and F2) were independently evaluated in a compact family block design in 2017 rainy and 2018 summer seasons. ANOVA revealed highly significant mean squares (p < 0.01) among different generations for grain Fe and Zn contents. Six-parameter generation mean analyses revealed a predominance of additive genetic effect and a significant (p < 0.05) additive × dominant interaction for the grain Fe content. The additive genetic effect for the grain Zn content was also highly significant (p < 0.01). However, interaction effects contributed minimally with respect to most of the crosses for the grain Zn content and hence we assume that a simple digenic inheritance pattern holds true for it. Furthermore, we established that narrow-sense heritability was high for the grain Fe content (>61.78%), whereas it was low to moderate for the grain Zn content (30.60-59.04%). The lack of superior parent heterosis coupled with non-significant inbreeding depression for Fe and Zn contents in grains further confirmed the predominance of an additive genetic effect. These findings will contribute to strategizing a comprehensive breeding method to exploit the available variability of grain Fe and Zn contents for the development of biofortified hybrids of pearl millet.

Identification of High-Yielding Iron-Biofortified Open-Pollinated Varieties of Pearl Millet in West Africa.

Pearl millet is a predominant food and fodder crop in West Africa. This study was carried out to test the newly developed open-pollinated varieties (OPVs) for field performance and stability for grain yield, grain iron (Fe), and grain zinc (Zn) contents across 10 locations in West Africa (i.e., Niger, Nigeria, Mali, Burkina Faso, Senegal, and Ghana). The test material consisted of 30 OPVs, of which 8 are Fe/Zn biofortified. The experiment was conducted in a randomized complete block design in three replications. ANOVA revealed highly significant variability for grain yield and micronutrient traits. The presence of genotype × environment (G × E) indicated that the expressions of traits are significantly influenced by both genetic and G × E factors, for grain Fe and Zn contents. Days to 50% flowering and plant height showed less G × E, suggesting these traits are largely under genetic control. The genotypes CHAKTI (46 days), ICTP 8203 (46 days), ICMV 177002 (50 days), ICMV 177003 (48 days), and Moro (53 days) had exhibited early flowering across locations leading to early physiological maturity. CHAKTI (1.42 t/ha yield; 62.24 mg/kg of grain Fe, 47.29 mg/kg of grain Zn) and ICMP 177002 (1.19 t/ha yield, 62.62 mg/kg of grain Fe, 46.62 mg/kg of grain Zn) have performed well for grain yield and also for micronutrients, across locations, compared with the check. Additive Main Effect and Multiplicative Interaction (AMMI) ANOVA revealed the highly significant genotypic differences, the mean sum of squares of environment, and its interaction with the genotypes. Based on the AMMI stability value (ASV), the most stable genotype is SOSAT-C88 (ASV = 0.04) for grain yield and resistance to downy mildew; mean grain yield and stability rankings (YSI) revealed that the genotypes CHAKTI, SOSAT-C88, and ICMV IS 99001 were high yielding and expressed stability across regions. The strong correlation (r = 0.98∗∗) of grain Fe and Zn contents that merits Fe-based selection is highly rewarding. CHAKTI outperformed over other genotypes for grain yield (71% higher), especially with early maturing varieties in West Africa, such as GB 8735, LCIC 9702, and Jirani, and for grain Fe (16.11% higher) and Zn (7% higher) contents across locations, and made a candidate of high-iron variety to be promoted for combating the micronutrient malnutrition in West and Central Africa (WCA).

Harnessing Sorghum Landraces to Breed High-Yielding, Grain Mold-Tolerant Cultivars With High Protein for Drought-Prone Environments.

Intermittent drought and an incidence of grain mold disease are the two major constraints affecting sorghum production and productivity. The study aimed at developing drought-tolerant sorghum varieties possessing a high protein content and tolerance to grain mold with stable performance using additive main effects and multiplicative interaction (AMMI) and genotype and genotype × environment interaction (GGE) biplot methods. Systematic hybridization among the 11 superior landraces resulted in subsequent pedigree-based breeding and selection from 2010 to 2015 evolved 19 promising varieties of grains such as white, yellow, and brown pericarp grains. These grain varieties were evaluated for their adaptability and stability for yield in 13 rainfed environments and for possessing tolerance to grain mold in three hot spot environments. A variety of yellow pericarp sorghum PYPS 2 (3,698 kg/ha; 14.52% protein; 10.70 mg/100 g Fe) possessing tolerance to grain mold was identified as a stable variety by using both AMMI and GGE analyses. Four mega-environments were identified for grain yield and fodder yield. Sorghum varieties PYPS 2, PYPS 4, PYPS 8, and PYPS 11 were highly stable in E2 with a low grain mold incidence. Besides meeting the nutritional demand of smallholder farmers under dryland conditions, these varieties are suitable for enhancing sorghum productivity under the present climate change scenario.

Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain.

Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.