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Background Pearl millet ( Pennisetum glaucum ) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 ( Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress response. Currently, no reports are available on the functions of the NAC family in pearl millet. Results Our genome-wide analysis found 151 NAC transcription factor genes ( PgNAC s) in the pearl millet genome. Thirty-eight and 76 PgNACs were found to be segmental and dispersed duplicated respectively. Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (− 073, − 29, and − 151) were found to be membrane-associated transcription factors. Seventeen other conserved motifs were found in PgNACs . Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. In total, 88 microRNA target sites were predicted in 59 PgNACs . A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNAC s are affected by salinity stress and drought stress, respectively. The expression of 36 randomly selected PgNAC s were examined by quantitative reverse transcription-PCR. Many of these genes showed diverse salt- and drought-responsive expression patterns in roots and leaves. These results confirm that PgNACs are potentially involved in regulating abiotic stress tolerance in pearl millet. Conclusion The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. Many of these genes are either upregulated or downregulated by either salinity or drought stress and may therefore contribute to establishing stress tolerance in pearl millet.

Downy mildew of pearl millet caused by the biotrophic oomycete Sclerospora graminicola is the most devastating disease which impairs pearl millet production causing huge yield and monetary losses. Chitosan nanoparticles (CNP) were synthesized from low molecular weight chitosan having higher degree of acetylation was evaluated for their efficacy against downy mildew disease of pearl millet caused by Sclerospora graminicola. Laboratory studies showed that CNP seed treatment significantly enhanced pearl millet seed germination percentage and seedling vigor compared to the control. Seed treatment with CNP induced systemic and durable resistance and showed significant downy mildew protection under greenhouse conditions in comparison to the untreated control. Seed treatment with CNP showed changes in gene expression profiles wherein expression of genes of phenylalanine ammonia lyase, peroxidase, polyphenoloxidase, catalase and superoxide dismutase were highly upregulated. CNP treatment resulted in earlier and higher expression of the pathogenesis related proteins PR1 and PR5. Downy mildew protective effect offered by CNP was found to be modulated by nitric oxide and treatment with CNP along with NO inhibitors cPTIO completely abolished the gene expression of defense enzymes and PR proteins. Further, comparative analysis of CNP with Chitosan revealed that the very small dosage of CNP performed at par with recommended dose of Chitosan for downy mildew management.

Apomixis is a naturally occurring mode of asexual reproduction in flowering plants that results in seed formation without the involvement of meiosis or fertilization of the egg. Seeds formed on an apomictic plant contain offspring genetically identical to the maternal plant. Apomixis has significant potential for preserving hybrid vigor from one generation to the next in highly productive crop plant genotypes. ApomicticPennisetum/Cenchrusspecies, members of the Poaceae (grass) family, reproduce by apospory. Apospory is characterized by apomeiosis, the formation of unreduced embryo sacs derived from nucellar cells of the ovary and, by parthenogenesis, the development of the unreduced egg into an embryo without fertilization. InPennisetum squamulatum (L.) R.Br., apospory segregates as a single dominant locus, the aposporyspecific genomic region (ASGR). In this study, we demonstrate that thePsASGR-BABY BOOM-like(PsASGR-BBML) gene is expressed in egg cells before fertilization and can induce parthenogenesis and the production of haploid offspring in transgenic sexual pearl millet. A reduction ofPsASGR-BBMLexpression in apomictic F₁ RNAi transgenic plants results in fewer visible parthenogenetic embryos and a reduction of embryo cell number compared with controls. Our results endorse a key role forPsASGR-BBMLin parthenogenesis and a newly discovered role for a member of the BBM-like clade of APETALA 2 transcription factors. Induction of parthenogenesis byPsASGR-BBMLwill be valuable for installing parthenogenesis to synthesize apomixis in crops and will have further application for haploid induction to rapidly obtain homozygous lines for breeding.

Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.

Excessive phosphorus (P) levels can disrupt nutrient balance in plants, adversely affecting growth. The molecular responses of Pennisetum species to high phosphorus stress remain poorly understood. This study examined two Pennisetum species, Pennisetum americanum × Pennisetum purpureum and Pennisetum americanum , under varying P concentrations (200, 600 and 1000 µmol·L − 1 KH 2 PO 4 ) to elucidate transcriptomic alterations under high-P conditions. Our findings revealed that P. americanum exhibited stronger adaption to high-P stress compared to P. americanum × P. purpureum . Both species showed an increase in plant height and leaf P content under elevated P levels, with P. americanum demonstrating greater height and higher P content than P. americanum × P. purpureum . Transcriptomic analysis identified significant up- and down-regulation of key genes (e.g. SAUR , GH3 , AHP , PIF4 , PYL , GST , GPX , GSR , CAT , SOD1 , CHS , ANR , P5CS and PsbO ) involved in plant hormone signal transduction, glutathione metabolism, peroxisomes, flavonoid biosynthesis, amino acid biosynthesis and photosynthesis pathways. Compared with P. americanum × P. purpureum , P. americanum has more key genes in the KEGG pathway, and some genes have higher expression levels. These results contribute valuable insights into the molecular mechanisms governing high-P stress in Pennisetum species and offer implications for broader plant stress research.

Pearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32–120 mg kg−1, Zn: 19–87 mg kg−1, PC: 8–16%), heritability (hbs2 ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, ‘Late embryogenesis abundant protein’, ‘Myb domain’, ‘pentatricopeptide repeat’, and ‘iron ion binding’ coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.

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.

The Yarlung Zangbo River Basin in China has a perennial grass species, Pennisetum centrasiaticum , which shows potential for improving feed quality. Researchers assembled two distinct collections, designated P. centrasiaticum —DB and P. centrasiaticum —NB, to investigate the growth characteristics and genetic variations within this species. Their objective was to comprehend the variance in phenotypic features and to sequence whole chloroplast genomes, which would illuminate evolutionary relationships and possibilities for selective breeding. The scientists assessed both agronomic and nutritional aspects of the grass and used sophisticated high-throughput methods to sequence the whole chloroplast genomes. P. centrasiaticum —DB demonstrated beneficial traits, including increased height (71.58 cm), a greater number of internodes (4.17), elongated ears (9.33 cm), an elevated ear weight ratio (7.91%), and higher ether extract content (16.40%), alongside reduced crude fiber content (386.30 g/kg), indicating improved palatability. The chloroplast genomes of P. centrasiaticum —DB (138,291 bp) and P. centrasiaticum —NB (138,283 bp) exhibited standard four-part architectures, with minor variations in the LSC, SSC, IR sections, GC content, and SSR distribution. A phylogenetic study classified Pennisetum and Cenchrus into separate clades, confirming their distinction at the species level. The differences in agronomic data and chloroplast genome data further clarify the distinctions between these two types of P. centrasiaticum , providing theoretical support for their future utilization. The P. centrasiaticum —DB germplasm has significant potential for producing high-quality fodder, while the chloroplast genome data provide fresh insights into the evolutionary linkages and molecular evolution of Pennisetum species.

Main conclusionPearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet.Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.

The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica , which requires host-released hormones, called strigolactones (SLs), for seed germination. Herein, we identify four SLs present in the Striga-susceptible line SOSAT-C88-P10 (P10) but absent in the resistant 29Aw (Aw). We generate chromosome-scale genome assemblies, including four gapless chromosomes for each line. The Striga-resistant Aw lacks a 0.7 Mb genome segment containing two putative CARLACTONOIC ACID METHYLTRANSFERASE1 ( CLAMT1 ) genes, which may contribute to SL biosynthesis. Functional assays show that P10CLAMT1b produces the SL-biosynthesis intermediate methyl carlactonoate (MeCLA) and that MeCLA is the precursor of P10-specific SLs. Screening a diverse pearl millet panel confirms the pivotal role of the CLAMT1 section for SL diversity and Striga susceptibility. Our results reveal a reason for Striga susceptibility in pearl millet and pave the way for generating resistant lines through marker-assisted breeding or direct genetic modification. Production of pearl millet is impacted by the root parasitic weed Striga hermonthica . Here, the authors assemble the genomes of resistant and susceptible lines of pearl millet and identify a critical gene CARLACTONOIC ACID METHYLTRANSFERASE1b ( CLAMT1b ) in determining Striga resistance.