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

Functional dissection of the chickpea (Cicer arietinum l.) stay-green phenotype associated with molecular variation at an ortholog of mendel’s i gene for cotyledon color: Implications for crop production and carotenoid biofortification

“Stay-green” crop phenotypes have been shown to impact drought tolerance and nutritional content of several crops. We aimed to genetically describe and functionally dissect the particular stay-green phenomenon found in chickpeas with a green cotyledon color of mature dry seed and investigate its potential use for improvement of chickpea environmental adaptations and nutritional value. We examined 40 stay-green accessions and a set of 29 BC2F4-5 stay-green introgression lines using a stay-green donor parent ICC 16340 and two Indian elite cultivars (KAK2, JGK1) as recurrent parents. Genetic studies of segregating populations indicated that the green cotyledon trait is controlled by a single recessive gene that is invariantly associated with the delayed degreening (extended chlorophyll retention). We found that the chickpea ortholog of Mendel’s I locus of garden pea, encoding a SGR protein as very likely to underlie the persistently green cotyledon color phenotype of chickpea. Further sequence characterization of this chickpea ortholog CaStGR1 (CaStGR1, for carietinum stay-green gene 1) revealed the presence of five different molecular variants (alleles), each of which is likely a loss-of-function of the chickpea protein (CaStGR1) involved in chlorophyll catabolism. We tested the wild type and green cotyledon lines for components of adaptations to dry environments and traits linked to agronomic performance in different experimental systems and different levels of water availability. We found that the plant processes linked to disrupted CaStGR1 gene did not functionality affect transpiration efficiency or water usage. Photosynthetic pigments in grains, including provitaminogenic carotenoids important for human nutrition, were 2–3-fold higher in the stay-green type. Agronomic performance did not appear to be correlated with the presence/absence of the stay-green allele. We conclude that allelic variation in chickpea CaStGR1 does not compromise traits linked to environmental adaptation and agronomic performance, and is a promising genetic technology for biofortification of provitaminogenic carotenoids in chickpea

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 droughtadaptive 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), markertrait 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

Association between winter anthocyanin production and drought stress in angiosperm evergreen species

Leaves of many evergreen angiosperm species turn red under high light during winter due to the production of anthocyanin pigments, while leaves of other species remain green. There is currently no explanation for why some evergreen species exhibit winter reddening while others do not. Conditions associated with low leaf water potentials (Ψ) have been shown to induce reddening in many plant species. Because evergreen species differ in susceptibility to water stress during winter, it is hypothesized that species which undergo winter colour change correspond with those that experience/tolerate the most severe daily declines in leaf Ψ during winter. Six angiosperm evergreen species which synthesize anthocyanin in leaves under high light during winter and five species which do not were studied. Field Ψ, pressure/volume curves, and gas exchange measurements were derived in summer (before leaf colour change had occurred) and winter. Consistent with the hypothesis, red-leafed species as a group had significantly lower midday Ψ in winter than green-leafed species, but not during the summer when all the leaves were green. However, some red-leafed species showed midday declines similar to those of green-leafed species, suggesting that low Ψ alone may not induce reddening. Pressure–volume curves also provided some evidence of acclimation to more negative water potentials by red-leafed species during winter (e.g. greater osmotic adjustment and cell wall hardening on average). However, much overlap in these physiological parameters was observed as well between red and green-leafed species, and some of the least drought-acclimated species were red-leafed. No difference was observed in transpiration (E) during winter between red and green-leaved species. When data were combined, only three of the six red-leafed species examined appeared physiologically acclimated to prolonged drought stress, compared to one of the five green-leafed species. This suggests that drought stress alone is not sufficient to explain winter reddening in evergreen angiosperms

Functional Dissection of the Chickpea (Cicer arietinum L.) Stay-Green Phenotype Associated with Molecular Variation at an Ortholog of Mendel’s I Gene for Cotyledon Color: Implications for Crop Production and Carotenoid Biofortification

“Stay-green” crop phenotypes have been shown to impact drought tolerance and nutritional content of several crops. We aimed to genetically describe and functionally dissect the particular stay-green phenomenon found in chickpeas with a green cotyledon color of mature dry seed and investigate its potential use for improvement of chickpea environmental adaptations and nutritional value. We examined 40 stay-green accessions and a set of 29 BC2F4-5 stay-green introgression lines using a stay-green donor parent ICC 16340 and two Indian elite cultivars (KAK2, JGK1) as recurrent parents. Genetic studies of segregating populations indicated that the green cotyledon trait is controlled by a single recessive gene that is invariantly associated with the delayed degreening (extended chlorophyll retention). We found that the chickpea ortholog of Mendel’s I locus of garden pea, encoding a SGR protein as very likely to underlie the persistently green cotyledon color phenotype of chickpea. Further sequence characterization of this chickpea ortholog CaStGR1 (CaStGR1, for carietinum stay-green gene 1) revealed the presence of five different molecular variants (alleles), each of which is likely a loss-of-function of the chickpea protein (CaStGR1) involved in chlorophyll catabolism. We tested the wild type and green cotyledon lines for components of adaptations to dry environments and traits linked to agronomic performance in different experimental systems and different levels of water availability. We found that the plant processes linked to disrupted CaStGR1 gene did not functionality affect transpiration efficiency or water usage. Photosynthetic pigments in grains, including provitaminogenic carotenoids important for human nutrition, were 2–3-fold higher in the stay-green type. Agronomic performance did not appear to be correlated with the presence/absence of the stay-green allele. We conclude that allelic variation in chickpea CaStGR1 does not compromise traits linked to environmental adaptation and agronomic performance, and is a promising genetic technology for biofortification of provitaminogenic carotenoids in chickpea

Safflower (Carthamus tinctorius L.) crop adaptation to residual moisture stress: conserved water use and canopy temperature modulation are better adaptive mechanisms

Oilseeds with high productivity and tolerance to various environmental stresses are in high demand in the food and industrial sectors. Safflower, grown under residual moisture in the semi-arid tropics, is adapted to moisture stress at certain levels. However, a substantial reduction in soil moisture has a significant impact on its productivity. Therefore, assessing genetic variation for water use efficiency traits like transpiration efficiency (TE), water uptake, and canopy temperature depression (CTD) is essential for enhancing crop adaptation to drought. The response of safflower genotypes (n = 12) to progressive soil moisture depletion was studied in terms of water uptake, TE, and CTD under a series of pot and field experiments. The normalised transpiration rate (NTR) in relation to the fraction of transpirable soil water (FTSW) varied significantly among genotypes. The genotypes A-1, Bhima, GMU-2347, and CO-1 had higher NTR-FTSW threshold values of 0.79 (R2 = 0.92), 0.74 (R2 = 0.96), 0.71 (R2 = 0.96), and 0.71 (R2 = 0.91), respectively, whereas GMU-2644 had the lowest 0.38 (R2 = 0.93). TE was high in genotype GMU-2347, indicating that it could produce maximum biomass per unit of water transpired. At both the vegetative and reproductive stages, significant positive relationships between TE, SPAD chlorophyll metre reading (SCMR) (p < 0.01) and CTD (p < 0.01) were observed under field conditions by linear regression. The genotypes with high FTSW-NTR thresholds, high SCMR, and low CTD may be useful clues in identifying a genotype’s ability to adapt to moisture stress. The findings showed that the safflower genotypes A-1, Bhima, GMU-2347, and CO-1 exhibited an early decline and regulated water uptake by conserving it for later growth stages under progressive soil water depletion

Modelling the effect of plant water use traits on yield and stay-green expression in sorghum

Post-rainy sorghum (Sorghum bicolor (L.) Moench) production underpins the livelihood of millions in the semiarid tropics, where the crop is affected by drought. Drought scenarios have been classified and quantified using crop simulation. In this report, variation in traits that hypothetically contribute to drought adaptation (plant growth dynamics, canopy and root water conducting capacity, drought stress responses) were virtually introgressed into the most common post-rainy sorghum genotype, and the influence of these traits on plant growth, development, and grain and stover yield were simulated across different scenarios. Limited transpiration rates under high vapour pressure deficit had the highest positive effect on production, especially combined with enhanced water extraction capacity at the root level. Variability in leaf development (smaller canopy size, later plant vigour or increased leaf appearance rate) also increased grain yield under severe drought, although it caused a stover yield trade-off under milder stress. Although the leaf development response to soil drying varied, this trait had only a modest benefit on crop production across all stress scenarios. Closer dissection of the model outputs showed that under water limitation, grain yield was largely determined by the amount of water availability after anthesis, and this relationship became closer with stress severity. All traits investigated increased water availability after anthesis and caused a delay in leaf senescence and led to a ‘stay-green’ phenotype. In conclusion, we showed that breeding success remained highly probabilistic; maximum resilience and economic benefits depended on drought frequency. Maximum potential could be explored by specific combinations of traits

Dual-Purpose Sorghum: A Targeted Sustainable Crop-Livestock Intervention for the Smallholder Subsistence Farming Communities of Adilabad, India

Sorghum plays an important role in the mixed crop–livestock system of tribal farming communities in Adilabad District, a high climate risk-prone region in India. Currently, the local seed system is limited to landraces and hybrids that are primarily used for domestic grain and fodder purposes. This study aimed to understand the farmers’ needs and context, and use this knowledge to deliver relevant, adoptable climate-smart sorghum crop technologies through farmer-participatory approaches (FPAs). We conducted an ex-ante survey with 103 farmer households to understand their preferences and constraints concerning sorghum, their staple food-crop. Farmers expressed taste as the most important characteristic, followed by stover yield, grain yield, drought adaptation, and pest resistance. They identified fodder deficit, loss of seed purity in landraces, and lack of diverse sorghum seed options as critical constraints. Therefore, we chose dual-purpose, open-pollinated sorghum varieties suitable for postrainy/rabi cultivation as the study site’s entry point. Accordingly, sixteen popular rabi sorghum varieties were tested at ICRISAT station (2017–18 and 2018–19) for agronomic performance in field conditions under a range of treatments (irrigation and fertilization). The standing crop was also scored by farmer representatives. Additionally, the detailed lysifield study elucidated the plant functions underlying the crop agronomic performance under water stress (plant water use and stay-green score) and an important trait of farmer’s interest (relation between stay-green score and in-vitro stover digestibility and relation between grain fat and protein content) The selected varieties– Phule Chitra, CSV22, M35-1 and preferred landrace (Sevata jonna)–were further tested with 21 farmers at Adilabad (2018–20). Participating farmers from both the trials and focus group discussions voiced their preference and willingness to adopt Phule Chitra and CSV22. This article summarizes how system-relevant crop options were selected for subsistence farmers of Adilabad and deployed using participatory approaches. While varieties are developed for wider adoption, farmers adopt only those suitable for their farm, household, and accessible market. Therefore, we strongly advocate FPA for developing and delivering farmer relevant crop technologies as a vehicle to systematically break crop adoption barriers and create a positive impact on household diets, well-being, and livelihoods, especially for smallholder subsistence farmers