Genetic diversity analysis of Azerbaijani bread wheat (Triticum aestivum L.) genotypes with simple sequence repeat markers linked to drought tolerance

Water stress causes large agricultural losses worldwide and deteriorates its quality. Drought tolerance in plants is a complex trait governed by multigenes and infleunce of various environmental factors affecting the expression of these genes. Thus this complexity necessitates the application of new molecular methods to identify and develop drought tolerant genotypes. The present study was conducted to investigate the genetic diversity of 45 Azerbaijani wheat (Triticum aestivum L.) core collection genotypes utilizing simple sequence repeat (SSR) markers associated with drought tolerance. Our results showed that nine primers out of twelve showed polymorphism. Maximum number of alleles were detected for WMC177 marker (on chromosome 2A), WMC 264 (on chromosome 3A) and WMC219 (on chromosome 4A) with 5, 5 and 4 alleles, respectively. The lowest alleles were determined for WMC219 marker (chromosome 4A) with only one allele. The total number of the detected alleles on A and D genome was 18 and 11 respectively. The maximum number of unique bands (3) was scored with pimer WMC 177. Seven genotypes (cv Gobustan, and Gizil bugda, landrace 6262, and research materials 6170, 6286, 6296 and 6293) possessed unique bands. Based on polymorphism analysis of the wheat genotypes by SSR markers, drought tolerant genotypes for utilization in breeding programs were selected

Soil property and crop yield responses to variation in land use and topographic position: Case study from southern highland of Ethiopia

Understanding soil property and crop yield responses to variations in land use and topographic gradient is vital for designing targeted soil and agronomic management practices. This study investigated the interrelationships between land use, topographic position, soil properties, and crop yield. Three replicates of three land use types - enset agroforestry, cropland (annual crop), and grazing land - were selected along a toposequence (upper, middle and lower) for the study. A total of 54 composite soil samples were collected and analyzed. Grain yield and above ground biomass were also gathered from the cropland and analyzed. Soil profile descriptions revealed notable variations in soil physical properties, including soil texture, bulk density, color, horizons, and depth among the pedons of the three topographic positions. Clay and silt fractions exhibited significant differences between land uses and topographic positions, while the sand fraction was influenced by topographic position alone. Crop and grazing lands displayed higher clay content compared to the enset field. A decreasing trend in clay fraction was observed from upper to lower topographic positions. The enset field had significantly higher soil pH, OC, TN, and K+ contents than crop field. A significantly higher available P of 16.61 mg kg−1 was measured from lower slope position followed by 14.08 mg kg−1 in middle slope. The upper slope position had the highest exchangeable acidity of 3.09 cmol(+) kg−1), followed by middle slope with 2.77 cmol(+) kg−1), 2.45 cmol(+) kg−1) in the lower slope position. Grain yield and above ground biomass decreased from lower slope to middle slope and upper slope positions. These observed variations in soil properties and crop yield among land uses and topographic positions underscore the necessity for tailored soil management strategies and agronomic practices specific to land use types and the specific localized topographic conditions to optimize agricultural productivity

Genetic analysis of purple pigmentation in rice seed and vegetative parts — implications on developing high-yielding purple rice (Oryza sativa L.)

Pigmentation in rice grains is an important quality parameter. Purple-coloured rice (Oryza sativa L.) indicates the presence of high anthocyanin with benefits of antioxidant properties. However, the genetic mechanism of grain colour is not fully understood. Therefore, the study focused on understanding pigmentation in grain pericarp and vegetative parts, and its relationship with blast resistance and enhanced grain yield. Three local cultivars from the northeastern region (NER) of India — Chakhao Poireiton (purple), Mang Meikri (light brown), and Kala Joha (white) — along with high-yielding varieties (HYVs) Shasharang (light brown) and Sahbhagi dhan (white) were used to develop biparental populations. The findings suggested that pigmentation in vegetative tissue was governed by the inter-allelic interaction of several genes. Haplotype analysis revealed that Kala3 complemented Kala4 in enhancing purple pigmentation and that Kala4 is not the only gene responsible for purple colour as evident by the presence of a desired allele for markers RID3 and RID4 (Kala4 locus) in Chakhao Poireiton and Kala Joha irrespective of their pericarp colour, implying the involvement of some other additional, unidentified genes/loci. RID3 and RID4 together with RM15191 (Kala3 locus) could be employed as a reliable marker set for marker-assisted selection (MAS). Pericarp colour was strongly correlated with colour in different vegetative parts, but showed a negative correlation with grain yield. Pb1, reported to be associated with panicle blast resistance, contributed to leaf blast resistance. Transgressive segregants for improved pigmentation and high yield were identified. The selection of lines exhibiting coloured pericarp, high anthocyanin content, aroma, blast resistance, and increased yield compared to their respective HYV parents will be valuable resources in the rice breeding programme

Vulnerability and resilience in the face of climate changes in Senegal's drylands: measurement at the household level and determinant assessment

The resilience capacity of smallholder households is one of the main drivers of their ability to continue to farm and make investments in the fragile dryland regions. This paper aims to assess the resilience profile of smallholder farmers in the face of climate change and the factors influencing it in three dryland sub-regions of Senegal, namely, Louga, Kaffrine, and Thies. We developed a composite index of climate resilience (CICR) using data on farmers' perceptions of climate variability and their perceived ability to withstand, adapt, and bounce back in the event of climatic shocks. Drought, strong winds, and soil fertility decline because of climate change emerged as the main climate hazards impacting smallholder farming systems. The CICR value ranged from −2 for the most vulnerable households to +2 for the most resilient households. On average, all the households were found to be vulnerable, with an average CICR value of −0.2. The LOUGA region was the most vulnerable, with an average CICR value of −0.36, followed by THIES (-0.2). The KAFFRINE region was relatively less vulnerable, with a CICR value of −0.1. Ordered logit model estimates show that the chances of improving CICR decrease with the increase of the household head's age until 59 years. Access to training on climate-smart agricultural (CSA) practices and climate information appeared to have the potential to increase by 171% the chance of the household improving its resilience status. Analysis also shows that one more woman working off-farm or in-home gardening has the potential to multiply by four times the chances of households being more resilient. This highlights the importance of empowering women to enhance household resilience to climate change. The off-farm revenue increased the chance to improve the resilience status of the farm household by 62% and the receipt of transfer revenue by 50%. This study provides a robust method for quantifying resilience or wellbeing and its drivers and enriches our understanding of the resilience ability of farmers to climate change in a West African context. It can be useful in designing effective adaptation interventions and improving the overall wellbeing of smallholder farmers

Milestones in Biology, Genetics, and Breeding of Pearl Millet

Pearl millet is a fascinating species for conducting basic research in biology and genetics; and for applied research in breeding. With a small number of large somatic chromosomes, pearl millet lends itself to investigation in classical and molecular cytogenetics. Its short life cycle, protogynous flowers and ability to set a large number of seeds per panicle make pearl millet highly suitable for studying flow of genes between cultivated annual species and related wild species. Centre of origin, domestication, primary and secondary gene pools of pearl millet helped in selection of suitable geographical area for collecting unique and diverse germplasm resources. The outcrossing nature of pearl millet provided the basis of exploitation of heterosis at commercial scale. Another important discovery related to pollination of pearl millet was role of pollen in reducing the infection of ovary by pathogens of ergot and smut. Knowledge of photoperiod response helped in extending the crop cultivation in new seasons and geographical regions; in controlling flowering in order to facilitate hybridization; and in selecting suitable sites for offseason nurseries. Outcrossing rate of above 85%, ease of inbred development, discovery of cytoplasmic male sterility and fertility restorer genes, lack of any negative association of cytoplasmic male sterility with growth and development, diseases and insect-pests, expression of positive and high magnitude of heterosis in productivity of hybrids and economic seed production provided a perfect platform for commercial exploitation of heterosis in pearl millet for the benefit of farming community. The genome of a reference genotype Tift 23D2B1-P1-P5 has been reported to contain an estimated 38,579 genes. Thus, a good understanding of biology and genetics of pearl millet has helped tremendously in breeding for higher productivity and stability

Comparative transcriptome analysis of respiration-related genes in nodules of phosphate-deficient soybean (Glycine max cv. Williams 82)

A transcriptome analysis was used to compare the nodule transcriptomes of the model soybean ‘Williams 82’ inoculated with two Bradyrhizobium diazoefficiens strains (USDA110 vs. CB1809) under phosphate (Pi) deficiency. The entire dataset revealed a core set of low-Pi-responsive genes and recognized enormous differential transcriptional changes between the Pi-deprived USDA110-nodules and CB1809-nodules. The lower symbiotic efficiency of the Pi-starved USDA110 nodules was ascribed to the downregulation of an F1-ATPase gene engaged in oxidative phosphorylation, more likely contributing to diminished ATP production. To cope with energy shortage caused by Pi stress, the Pi-deprived USDA110-nodules preferentially upregulated the expression of a large number of genes encoding enzymes implicated in specialized energy-demanding pathways, such as the mitochondrial respiratory chain (i.e., cytochrome c oxidase), alcoholic fermentation (i.e., pyruvate decarboxylase and alcohol dehydrogenase) and glycolysis (e.g., hexokinase, phosphofructokinase, glyceraldehyde‐3‐phosphate dehydrogenase and pyruvate kinase). These respiratory adjustments were likely associated with higher metabolic cost and redox imbalance, thereby, negatively affecting nodule symbiosis under Pi deprivation. In contrast, the Pi-starved CB1809-nodules reduced the metabolic cost by regulating a lower number of genes and increasing the expression of genes encoding proteins implicated in non-phosphorylating bypasses (e.g., flavoprotein alpha and flavoprotein:ubiqionone oxidoreductase), which could promote the carbohydrate utilization efficiency and energy metabolism. Notably, the upregulation of a transcript encoding a malate dehydrogenase could boost the CB1809-nodules under Pi stress. The dynamic shifts in energy metabolism in the Pi-deprived USDA110-nodules and CB1809-nodules could be transformative to upgrade the mechanistic/conceptual understandings of soybean adaptation to Pi deficiency at the transcriptional level

Improving grain quality and nitrogen use efficiency of cereal-based cropping systems on vertisols in semi-arid tropics

Context Semi-arid tropics is facing serious issues of malnutrition in population owing to poor quality of food grain production. Malnutrition is directly linked to lower grain protein and zinc yield due to inappropriate land and water, and nutrient management practices, which also resulted into reduced nitrogen use efficiency (NUE) in cereals. Objective The objectives of the study were to evaluate the effect of land and water and nutrient management on grain protein and zinc yield, and NUE of cereal-based cropping systems on vertisols soils in semi-arid tropics. Methods The study was carried out at Hyderabad in India during 2014–15 and 2015–16 and involved three cropping systems (two rotation systems: sorghum-chickpea and maize-groundnut; and one intercropping: pearl millet + pigeonpea), two land and water management i.e. flatbed and broad bed furrows and four nutrient management-N1: Control (no fertilizer), N2: 100% recommended application of macronutrient (nitrogen, phosphorus and potassium) through chemical fertilizer, N3: N2 + 100% recommended application of secondary nutrient (sulphur) and micronutrient (zinc and boron) through chemical fertilizer, and N4 (integrated nutrient): 50% of N2 + 50% nitrogen in cereals or phosphorus in legumes through organic fertilizer as vermicompost. Results In sorghum-chickpea rotation system, the treatment interaction broad bed furrows with 100% recommended application of macronutrient, secondary nutrient and micronutrient recorded significantly higher grain zinc yield in both the years, while grain protein yield was significantly higher in second year. The grain protein and zinc yield in sorghum-chickpea rotation system, and agronomic nitrogen use efficiency in pearl millet+pigeonpea intercropping system was significantly higher in broad bed furrows than flatbed. The agronomic NUE of broad bed furrows was higher by 61% in 2014–15 and 65% in 2015–16 over flatbed. Among the nutrient management treatments, grain protein and zinc yield, and agronomic NUE were significantly higher in combined application of macronutrient, secondary nutrient, and micronutrients through chemical fertilizer i.e. N3 followed by N4, N2 and N1. Conclusion The broad bed furrows and application of macronutrient, secondary nutrient and micronutrient could be an effective integrated land and water and nutrient management approach to improve grain quality and agronomic nitrogen use efficiency of cereal-based cropping systems in semi-arid tropics. Implications This study contributed to develop integrated land and water and nutrient management as an innovative agronomic management practice for cereal-based cropping systems, which needs to scale-up through Government agricultural policies to overcome the issue of malnutrition in population living in semi-arid tropics

Ethylene regulates auxin-mediated root gravitropic machinery and controls root angle in cereal crops

Root angle is a critical factor in optimizing the acquisition of essential resources from different soil depths. The regulation of root angle relies on the auxin-mediated root gravitropism machinery. While the influence of ethylene on auxin levels is known, its specific role in governing root gravitropism and angle remains uncertain, particularly when Arabidopsis (Arabidopsis thaliana) core ethylene signaling mutants show no gravitropic defects. Our research, focusing on rice (Oryza sativa L.) and maize (Zea mays), clearly reveals the involvement of ethylene in root angle regulation in cereal crops through the modulation of auxin biosynthesis and the root gravitropism machinery. We elucidated the molecular components by which ethylene exerts its regulatory effect on auxin biosynthesis to control root gravitropism machinery. The ethylene-insensitive mutants ethylene insensitive2 (osein2) and ethylene insensitive like1 (oseil1), exhibited substantially shallower crown root angle compared to the wild type. Gravitropism assays revealed reduced root gravitropic response in these mutants. Hormone profiling analysis confirmed decreased auxin levels in the root tips of the osein2 mutant, and exogenous auxin (NAA) application rescued root gravitropism in both ethylene-insensitive mutants. Additionally, the auxin biosynthetic mutant mao hu zi10 (mhz10)/tryptophan aminotransferase2 (ostar2) showed impaired gravitropic response and shallow crown root angle phenotypes. Similarly, maize ethylene-insensitive mutants (zmein2) exhibited defective gravitropism and root angle phenotypes. In conclusion, our study highlights that ethylene controls the auxin-dependent root gravitropism machinery to regulate root angle in rice and maize, revealing a functional divergence in ethylene signaling between Arabidopsis and cereal crops. These findings contribute to a better understanding of root angle regulation and have implications for improving resource acquisition in agricultural systems

CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in pigeonpea and groundnut

The CRISPR/Cas9 technology, renowned for its ability to induce precise genetic alterations in various crop species, has encountered challenges in its application to grain legume crops such as pigeonpea and groundnut. Despite attempts at gene editing in groundnut, the low rates of transformation and editing have impeded its widespread adoption in producing genetically modified plants. This study seeks to establish an effective CRISPR/Cas9 system in pigeonpea and groundnut through Agrobacterium-mediated transformation, with a focus on targeting the phytoene desaturase (PDS) gene. The PDS gene is pivotal in carotenoid biosynthesis, and its disruption leads to albino phenotypes and dwarfism. Two constructs (one each for pigeonpea and groundnut) were developed for the PDS gene, and transformation was carried out using different explants (leaf petiolar tissue for pigeonpea and cotyledonary nodes for groundnut). By adjusting the composition of the growth media and refining Agrobacterium infection techniques, transformation efficiencies of 15.2% in pigeonpea and 20% in groundnut were achieved. Mutation in PDS resulted in albino phenotype, with editing efficiencies ranging from 4 to 6%. Sequence analysis uncovered a nucleotide deletion (A) in pigeonpea and an A insertion in groundnut, leading to a premature stop codon and, thereby, an albino phenotype. This research offers a significant foundation for the swift assessment and enhancement of CRISPR/Cas9-based genome editing technologies in legume crops