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Chu L, Yang K, Chen C, Zhao B, Hou Y, Wang W, Zhao P, Wang K, Wang B, Xiao Y, Li Y, Li Y, Song Q, Liu B, Fan R, Bohra A, Yu J, Sonnenschein EC, Varshney RK, Tian Z, Jian J, Wan P. Chromosome-level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2173-2185. [PMID: 38497586 PMCID: PMC11258975 DOI: 10.1111/pbi.14337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 02/22/2024] [Accepted: 03/02/2024] [Indexed: 03/19/2024]
Abstract
Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome-wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.
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Affiliation(s)
- Liwei Chu
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
- College of Life and HealthDalian UniversityDalianLiaoningChina
| | - Kai Yang
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
| | | | - Bo Zhao
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
| | - Yanan Hou
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
| | | | - Pu Zhao
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
| | - Kaili Wang
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
| | | | - Ying Xiao
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
| | - Yongqiang Li
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
| | - Yisong Li
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
| | - Qijian Song
- Soybean Genomics and Improvement LaboratoryBeltsville Agricultural Research Center, USDA‐ARSBeltsvilleMarylandUSA
| | - Biao Liu
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
| | - Ruoxi Fan
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
| | - Abhishek Bohra
- WA State Agricultural Biotechnology CentreCentre for Crop and Food Innovation, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Jianping Yu
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
| | | | - Rajeev K Varshney
- WA State Agricultural Biotechnology CentreCentre for Crop and Food Innovation, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Jianbo Jian
- BGI GenomicsBGI‐ShenzhenShenzhenChina
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Ping Wan
- College of Plant Science and TechnologyKey Laboratory of New Technology in Agricultural ApplicationBeijing University of AgricultureBeijingChina
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2
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Kambara K, Gupta SK, Takano T, Tsugama D. Data from collection and analysis of RNA sequencing data from pearl millet. Data Brief 2024; 55:110592. [PMID: 38993231 PMCID: PMC11237866 DOI: 10.1016/j.dib.2024.110592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 07/13/2024] Open
Abstract
Pearl millet (Pennisetum glaucum, also known as Cenchrus americanus) is a cereal crop that has a C4 photosynthesis system and that can grow and develop seeds even under stressed conditions including drought-stressed, high temperature-stressed and nutrient-poor conditions. In previous studies, transcriptomes of pearl millet were studied by RNA sequencing (RNA-Seq) to understand mechanisms regulating its development and tolerance to such stressed conditions. Here, RNA-Seq reads from 565 pearl millet samples from 25 projects in the NCBI (National Center for Biotechnology Information) BioProject database were collected and mapped to the pearl millet reference genome to obtain read counts and transcripts per million (TPM) for each pearl millet gene. The count and TPM data for all the 565 samples as well as the attributes of those samples and projects were deposited in the figshare repository (https://doi.org/10.6084/m9.figshare.24902100).
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Affiliation(s)
- Kota Kambara
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo 188-0002, Japan
| | - Shashi Kumar Gupta
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India
| | - Tetsuo Takano
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo 188-0002, Japan
| | - Daisuke Tsugama
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo 188-0002, Japan
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3
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Singh S, Yadav CB, Lubanga N, Hegarty M, Yadav RS. Genome-wide SNPs and candidate genes underlying the genetic variations for protein and amino acids in pearl millet (Pennisetum glaucum) germplasm. PLANTA 2024; 260:63. [PMID: 39068266 PMCID: PMC11283402 DOI: 10.1007/s00425-024-04495-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
MAIN CONCLUSION A total of 544 significant marker-trait associations and 286 candidate genes associated with total protein and 18 amino acids were identified. Thirty-three candidate genes were found near the strong marker trait associations (- log10P ≥ 5.5). Pearl millet (Pennisetum glaucum) is largely grown as a subsistence crop in South Asia and sub-Saharan Africa. It serves as a major source of daily protein intake in these regions. Despite its importance, no systematic effort has been made to study the genetic variations of protein and amino acid content in pearl millet germplasm. The present study was undertaken to dissect the global genetic variations of total protein and 18 essential and non-essential amino acids in pearl millet, using a set of 435 K Single Nucleotide Polymorphisms (SNPs) and 161 genotypes of the Pearl Millet Inbred Germplasm Association Panel (PMiGAP). A total of 544 significant marker-trait associations (at P < 0.0001; - log10P ≥ 4) were detected and 23 strong marker-trait associations were identified using Bonferroni's correction method. Forty-eight pleiotropic loci were found in the genome for the studied traits. In total, 286 candidate genes associated with total protein and 18 amino acids were identified. Thirty-three candidate genes were found near strongly associated SNPs. The associated markers and the candidate genes provide an insight into the genetic architecture of the traits studied and are going to be useful in breeding improved pearl millet varieties in the future. Availabilities of improved pearl millet varieties possessing higher protein and amino acid compositions will help combat the rising malnutrition problem via diet.
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Affiliation(s)
- Satbeer Singh
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK
- Division of Agrotechnology, Council of Scientific and Industrial Research (CSIR) - Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176 061, India
| | - Chandra Bhan Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK
- Department of Genetics, Genomics, and Breeding, NIAB-EMR, East Malling, ME19 6BJ, UK
| | - Nelson Lubanga
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK
| | - Matthew Hegarty
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK
| | - Rattan S Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3EE, UK.
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Adegbaju MS, Ajose T, Adegbaju IE, Omosebi T, Ajenifujah-Solebo SO, Falana OY, Shittu OB, Adetunji CO, Akinbo O. Genetic engineering and genome editing technologies as catalyst for Africa's food security: the case of plant biotechnology in Nigeria. Front Genome Ed 2024; 6:1398813. [PMID: 39045572 PMCID: PMC11263695 DOI: 10.3389/fgeed.2024.1398813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/15/2024] [Indexed: 07/25/2024] Open
Abstract
Many African countries are unable to meet the food demands of their growing population and the situation is worsened by climate change and disease outbreaks. This issue of food insecurity may lead to a crisis of epic proportion if effective measures are not in place to make more food available. Thus, deploying biotechnology towards the improvement of existing crop varieties for tolerance or resistance to both biotic and abiotic stresses is crucial to increasing crop production. In order to optimize crop production, several African countries have implemented strategies to make the most of this innovative technology. For example, Nigerian government has implemented the National Biotechnology Policy to facilitate capacity building, research, bioresource development and commercialization of biotechnology products for over two decades. Several government ministries, research centers, universities, and agencies have worked together to implement the policy, resulting in the release of some genetically modified crops to farmers for cultivation and Commercialization, which is a significant accomplishment. However, the transgenic crops were only brought to Nigeria for confined field trials; the manufacturing of the transgenic crops took place outside the country. This may have contributed to the suspicion of pressure groups and embolden proponents of biotechnology as an alien technology. Likewise, this may also be the underlying issue preventing the adoption of biotechnology products in other African countries. It is therefore necessary that African universities develop capacity in various aspects of biotechnology, to continuously train indigenous scientists who can generate innovative ideas tailored towards solving problems that are peculiar to respective country. Therefore, this study intends to establish the role of genetic engineering and genome editing towards the achievement of food security in Africa while using Nigeria as a case study. In our opinion, biotechnology approaches will not only complement conventional breeding methods in the pursuit of crop improvements, but it remains a viable and sustainable means of tackling specific issues hindering optimal crop production. Furthermore, we suggest that financial institutions should offer low-interest loans to new businesses. In order to promote the growth of biotechnology products, especially through the creation of jobs and revenues through molecular farming.
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Affiliation(s)
- Muyiwa Seyi Adegbaju
- Department of Crop, Soil and Pest Management, Federal University of Technology Akure, Akure, Ondo, Nigeria
| | - Titilayo Ajose
- Fruits and Spices Department, National Horticultural Institute, Ibadan, Oyo, Nigeria
| | | | - Temitayo Omosebi
- Department of Agricultural Technology, Federal College of Forestry, Jos, Nigeria
| | | | - Olaitan Yetunde Falana
- Department of Genetics, Genomic and Bioinformatics, National Biotechnology Research and Development Agency, Abuja, Nigeria
| | - Olufunke Bolatito Shittu
- Department of Microbiology, College of Biosciences, Federal University of Agriculture, Abeokuta, Nigeria
| | | | - Olalekan Akinbo
- African Union Development Agency-NEPAD, Office of Science, Technology and Innovation, Midrand, South Africa
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Khound R, Rajput SG, Schnable JC, Vetriventhan M, Santra DK. Genome-wide association study reveals marker-trait associations for major agronomic traits in proso millet (Panicum miliaceum L.). PLANTA 2024; 260:44. [PMID: 38963439 DOI: 10.1007/s00425-024-04465-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
MAIN CONCLUSION The pilot-scale genome-wide association study in the US proso millet identified twenty marker-trait associations for five morpho-agronomic traits identifying genomic regions for future studies (e.g. molecular breeding and map-based cloning). Proso millet (Panicum miliaceum L.) is an ancient grain recognized for its excellent water-use efficiency and short growing season. It is an indispensable part of the winter wheat-based dryland cropping system in the High Plains of the USA. Its grains are endowed with high nutritional and health-promoting properties, making it increasingly popular in the global market for healthy grains. There is a dearth of genomic resources in proso millet for developing molecular tools to complement conventional breeding for developing high-yielding varieties. Genome-wide association study (GWAS) is a widely used method to dissect the genetics of complex traits. In this pilot study of the first-ever GWAS in the US proso millet, 71 globally diverse genotypes of 109 the US proso millet core collection were evaluated for five major morpho-agronomic traits at two locations in western Nebraska, and GWAS was conducted to identify single nucleotide polymorphisms (SNPs) associated with these traits. Analysis of variance showed that there was a significant difference among the genotypes, and all five traits were also found to be highly correlated with each other. Sequence reads from genotyping-by-sequencing (GBS) were used to identify 11,147 high-quality bi-allelic SNPs. Population structure analysis with those SNPs showed stratification within the core collection. The GWAS identified twenty marker-trait associations (MTAs) for the five traits. Twenty-nine putative candidate genes associated with the five traits were also identified. These genomic regions can be used to develop genetic markers for marker-assisted selection in proso millet breeding.
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Affiliation(s)
- Rituraj Khound
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Santosh G Rajput
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Dryland Genetics Inc, Ames, IA, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Mani Vetriventhan
- Genebank, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Dipak K Santra
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
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Daduwal HS, Bhardwaj R, Srivastava RK. Pearl millet a promising fodder crop for changing climate: a review. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:169. [PMID: 38913173 DOI: 10.1007/s00122-024-04671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/05/2024] [Indexed: 06/25/2024]
Abstract
The agricultural sector faces colossal challenges amid environmental changes and a burgeoning human population. In this context, crops must adapt to evolving climatic conditions while meeting increasing production demands. The dairy industry is anticipated to hold the highest value in the agriculture sector in future. The rise in the livestock population is expected to result in an increased demand for fodder feed. Consequently, it is crucial to seek alternative options, as crops demand fewer resources and are resilient to climate change. Pearl millet offers an apposite key to these bottlenecks, as it is a promising climate resilience crop with significantly low energy, water and carbon footprints compared to other crops. Numerous studies have explored its potential as a fodder crop, revealing promising performance. Despite its capabilities, pearl millet has often been overlooked. To date, few efforts have been made to document molecular aspects of fodder-related traits. However, several QTLs and candidate genes related to forage quality have been identified in other fodder crops, which can be harnessed to enhance the forage quality of pearl millet. Lately, excellent genomic resources have been developed in pearl millet allowing deployment of cutting-edge genomics-assisted breeding for achieving a higher rate of genetic gains. This review would facilitate a deeper understanding of various aspects of fodder pearl millet in retrospect along with the future challenges and their solution. This knowledge may pave the way for designing efficient breeding strategies in pearl millet thereby supporting sustainable agriculture and livestock production in a changing world.
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Affiliation(s)
- Harmanpreet Singh Daduwal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Ruchika Bhardwaj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India.
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Liu X, Zhang N, Sun Y, Fu Z, Han Y, Yang Y, Jia J, Hou S, Zhang B. QTL mapping of downy mildew resistance in foxtail millet by SLAF‑seq and BSR-seq analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:168. [PMID: 38909331 DOI: 10.1007/s00122-024-04673-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 03/03/2024] [Indexed: 06/24/2024]
Abstract
KEY MESSAGE Key message Three major QTLs for resistance to downy mildew were located within an 0.78 Mb interval on chromosome 8 in foxtail millet. Downy mildew, a disease caused by Sclerospora graminicola, is a serious problem that jeopardizes the yield and quality of foxtail millet. Breeding resistant varieties represents one of the most economical and effective solutions, yet there is a lack of molecular markers related to the resistance. Here, a mapping population comprising of 158 F6:7 recombinant inbred lines (RILs) was constructed from the crossing of G1 and JG21. Based on the specific locus amplified fragment sequencing results, a high-density linkage map of foxtail millet with 1031 bin markers, spanning 1041.66 cM was constructed. Based on the high-density linkage map and the phenotype data in four environments, a total of nine quantitative trait loci (QTL) associated with resistance to downy mildew were identified. Further BSR-seq confirmed the genomic regions containing the potential candidate genes related to downy mildew resistance. Interestingly, a 0.78-Mb interval between C8M257 and C8M268 on chromosome 8 was highlighted because of its presence in three major QTL, qDM8_1, qDM8_2, and qDM8_4, which contains 10 NBS-LRR genes. Haplotype analysis in RILs and natural population suggest that 9 SNP loci on Seita8G.199800, Seita8G.195900, Seita8G.198300, and Seita.8G199300 genes were significantly correlated with disease resistance. Furthermore, we found that those genes were taxon-specific by collinearity analysis of pearl millet and foxtail millet genomes. The identification of these new resistance QTL and the prediction of resistance genes against downy mildew will be useful in breeding for resistant varieties and the study of genetic mechanisms of downy mildew disease resistance in foxtail millet.
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Affiliation(s)
- Xu Liu
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- Houji Laboratory in Shanxi Province, Taiyuan, 030031, Shanxi, China
| | - Nuo Zhang
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- Houji Laboratory in Shanxi Province, Taiyuan, 030031, Shanxi, China
| | - Yurong Sun
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- Houji Laboratory in Shanxi Province, Taiyuan, 030031, Shanxi, China
| | - Zhenxin Fu
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- Houji Laboratory in Shanxi Province, Taiyuan, 030031, Shanxi, China
| | - Yuanhuai Han
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China
- Houji Laboratory in Shanxi Province, Taiyuan, 030031, Shanxi, China
| | - Yang Yang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China
- Houji Laboratory in Shanxi Province, Taiyuan, 030031, Shanxi, China
| | - Jichun Jia
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- Houji Laboratory in Shanxi Province, Taiyuan, 030031, Shanxi, China
| | - Siyu Hou
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, China.
- Houji Laboratory in Shanxi Province, Taiyuan, 030031, Shanxi, China.
| | - Baojun Zhang
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
- Houji Laboratory in Shanxi Province, Taiyuan, 030031, Shanxi, China.
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8
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Patan SSVK, Vallepu S, Shaik KB, Shaik N, Adi Reddy NRY, Terry RG, Sergeant K, Hausman JF. Drought resistance strategies in minor millets: a review. PLANTA 2024; 260:29. [PMID: 38879859 DOI: 10.1007/s00425-024-04427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/26/2024] [Indexed: 07/03/2024]
Abstract
MAIN CONCLUSION The review discusses growth and drought-response mechanisms in minor millets under three themes: drought escape, drought avoidance and drought tolerance. Drought is one of the most prominent abiotic stresses impacting plant growth, performance, and productivity. In the context of climate change, the prevalence and severity of drought is expected to increase in many agricultural regions worldwide. Millets (coarse grains) are a group of small-seeded grasses cultivated in arid and semi-arid regions throughout the world and are an important source of food and feed for humans and livestock. Although minor millets, i.e., foxtail millet, finger millet, proso millet, barnyard millet, kodo millet and little millet are generally hardier and more drought-resistant than cereals and major millets (sorghum and pearl millet), understanding their responses, processes and strategies in response to drought is more limited. Here, we review drought resistance strategies in minor millets under three themes: drought escape (e.g., short crop cycle, short vegetative period, developmental plasticity and remobilization of assimilates), drought avoidance (e.g., root traits for better water absorption and leaf traits to control water loss), and drought tolerance (e.g., osmotic adjustment, maintenance of photosynthetic ability and antioxidant potential). Data from 'omics' studies are summarized to provide an overview of the molecular mechanisms important in drought tolerance. In addition, the final section highlights knowledge gaps and challenges to improving minor millets. This review is intended to enhance major cereals and millet per se in light of climate-related increases in aridity.
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Affiliation(s)
| | - Suneetha Vallepu
- Department of Botany, Yogi Vemana University, Kadapa, Andhra Pradesh, 516005, India
| | - Khader Basha Shaik
- Department of Botany, Yogi Vemana University, Kadapa, Andhra Pradesh, 516005, India
| | - Naseem Shaik
- Department of Botany, Yogi Vemana University, Kadapa, Andhra Pradesh, 516005, India
| | | | | | - Kjell Sergeant
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, (LIST), Avenue Des Hauts Fourneaux 5, Esch-Sur-Alzette, Luxembourg
| | - Jean François Hausman
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, (LIST), Avenue Des Hauts Fourneaux 5, Esch-Sur-Alzette, Luxembourg
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Silva QM, Andrade-Vieria LF. Is pearl millet (Pennisetum glaucum) a good plant species for ecotoxicological tests? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:41953-41963. [PMID: 38856851 DOI: 10.1007/s11356-024-33947-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Various plant species can be selected for environmental testing, including pearl millet (Pennisetum glaucum (L.) R. Br), a globally significant cereal crop. This study aims to assess millet's suitability as a species for ecotoxicological tests, examining (1) germination and initial development dynamics, (2) the minimum seed quantity for reliable sampling, (3) optimal experimental design with replication numbers, (4) suitability of positive control, and (5) the effectiveness of the protocol in evaluating toxic effects of environmental pollutants. Millet exhibited rapid and uniform germination as well as consistent initial seedling development. To establish the minimum number of seeds required for reliable experimentation, germination, and seedling growth were compared across plots containing 10, 25, and 50 seeds. Consequently, 10 seeds per plot were chosen for subsequent experiments to reduce labor and costs while maintaining reliability. To validate the selected experimental design, and to establish a positive control for assays, aluminum was used as a toxic element at concentrations ranging from 10-2 to 10-6 M. While aluminum did not affect the final percentage of germinated seeds, it did exhibit an impact on the Germination Speed Index (GSI). Significant differences in root and aerial growth, and with fresh weight, were observed. The 10-3M concentration was chosen as the positive control as the 10-2 concentration showed extreme toxicity. To assess the applicability of the established protocol in determining the toxic effects of environmental pollutants, millet roots were exposed to the toxic agents atrazine, cadmium, methyl methane sulfonate (MMS), and Spent pot liner (SPL). Millet demonstrated sensitivity and efficiency in response to these tests. In conclusion, millet proves to be an effective species for the toxicological risk assessment of environmental pollutants.
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Affiliation(s)
- Quênia Mara Silva
- Department of Biology, Natural Sciences Institute, Federal University of Lavras, PO Box 3037 - 37, Lavras, MG, 200-900, Brazil
| | - Larissa Fonseca Andrade-Vieria
- Department of Ecology and Conservation, Natural Sciences Institute, Federal University of Lavras, PO Box 3037 - 37, Lavras, MG, 200-900, Brazil.
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10
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Garg V, Barmukh R, Chitikineni A, Roorkiwal M, Ojiewo C, Bohra A, Thudi M, Singh VK, Kudapa H, Saxena RK, Fountain J, Mir RR, Bharadwaj C, Chen X, Xin L, Pandey MK. Celebrating Professor Rajeev K. Varshney's transformative research odyssey from genomics to the field on his induction as Fellow of the Royal Society. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1504-1515. [PMID: 38206288 PMCID: PMC11123405 DOI: 10.1111/pbi.14282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/17/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
Professor Rajeev K. Varshney's transformative impact on crop genomics, genetics, and agriculture is the result of his passion, dedication, and unyielding commitment to harnessing the potential of genomics to address the most pressing challenges faced by the global agricultural community. Starting from a small town in India and reaching the global stage, Professor Varshney's academic and professional trajectory has inspired many scientists active in research today. His ground-breaking work, especially his effort to list orphan tropical crops to genomic resource-rich entities, has been transformative. Beyond his scientific achievements, Professor Varshney is recognized by his colleagues as an exemplary mentor, fostering the growth of future researchers, building institutional capacity, and strengthening scientific capability. His focus on translational genomics and strengthening seed system in developing countries for the improvement of agriculture has made a tangible impact on farmers' lives. His skills have been best utilized in roles at leading research centres where he has applied his expertise to deliver a new vision for crop improvement. These efforts have now been recognized by the Royal Society with the award of the Fellowship (FRS). As we mark this significant milestone in his career, we not only celebrate Professor Varshney's accomplishments but also his wider contributions that continue to transform the agricultural landscape.
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Affiliation(s)
- Vanika Garg
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rutwik Barmukh
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Annapurna Chitikineni
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and BiotechnologyUnited Arab Emirates UniversityAl AinUAE
| | - Chris Ojiewo
- International Maize and Wheat Improvement Center (CIMMYT)NairobiKenya
| | - Abhishek Bohra
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | | | - Vikas K. Singh
- International Rice Research Institute (IRRI)‐South‐Asia HubInternational Crops Research Institute for the Semi‐Arid TropicsHyderabadIndia
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | - Jake Fountain
- Department of Plant PathologyUniversity of GeorgiaGriffinGeorgiaUSA
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of AgricultureSKUAST‐KashmirWaduraIndia
| | | | - Xiaoping Chen
- Crops Research InstituteGuangdong Academy of Agricultural Sciences (GDAAS)GuangzhouChina
| | | | - Manish K. Pandey
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
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11
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Hu Z, Chen J, Olatoye MO, Zhang H, Lin Z. Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum. THE PLANT GENOME 2024; 17:e20448. [PMID: 38602082 DOI: 10.1002/tpg2.20448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The gene expression landscape across different tissues and developmental stages reflects their biological functions and evolutionary patterns. Integrative and comprehensive analyses of all transcriptomic data in an organism are instrumental to obtaining a comprehensive picture of gene expression landscape. Such studies are still very limited in sorghum, which limits the discovery of the genetic basis underlying complex agricultural traits in sorghum. We characterized the genome-wide expression landscape for sorghum using 873 RNA-sequencing (RNA-seq) datasets representing 19 tissues. Our integrative analysis of these RNA-seq data provides the most comprehensive transcriptomic atlas for sorghum, which will be valuable for the sorghum research community for functional characterizations of sorghum genes. Based on the transcriptome atlas, we identified 595 housekeeping genes (HKGs) and 2080 tissue-specific expression genes (TEGs) for the 19 tissues. We identified different gene features between HKGs and TEGs, and we found that HKGs have experienced stronger selective constraints than TEGs. Furthermore, we built a transcriptome-wide co-expression network (TW-CEN) comprising 35 modules with each module enriched in specific Gene Ontology terms. High-connectivity genes in TW-CEN tend to express at high levels while undergoing intensive selective pressure. We also built global and seed-preferential co-expression networks of starch synthesis pathways, which indicated that photosynthesis and microtubule-based movement play important roles in starch synthesis. The global transcriptome atlas of sorghum generated by this study provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum.
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Affiliation(s)
- Zhenbin Hu
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Junhao Chen
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Marcus O Olatoye
- USDA-ARS, Forage Seed and Cereal Research Unit, Prosser, Washington, USA
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
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12
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Bhavani P, Nandini C, Maharajan T, Ningaraju TM, Nandini B, Parveen SG, Pushpa K, Ravikumar RL, Nagaraja TE, Ceasar SA. Brown-top millet: an overview of breeding, genetic, and genomic resources development for crop improvement. PLANTA 2024; 260:10. [PMID: 38796805 DOI: 10.1007/s00425-024-04446-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/19/2024] [Indexed: 05/29/2024]
Abstract
MAIN CONCLUSION Brown-top millet is a lesser-known millet with a high grain nutrient value, early maturation, and drought tolerance that needs basic research to understand and conserve food security. Brown-top millet [Urochloa ramosa (L.)] is currently cultivated in some developing countries (especially in India) for food and fodder, although it is less known among the small millets. Like other millets, it contains macro- and micronutrients, vitamins, minerals, proteins, and fiber, all of which have rich health benefits. The nutritional importance and health benefits of brown-top millet are still unknown to many people due to a lack of awareness, wide cultivation, and research. Hence, this millet is currently overshadowed by other major cereals. This review article aims to present the nutritional, breeding, genetic, and genomic resources of brown-top millet to inform millet and other plant researchers. It is important to note that genetic and genomic resources have not yet been created for this millet. To date, there are no genomic and transcriptomic resources for brown-top millet to develop single nucleotide polymorphisms (SNP) and insertion/Deletions (InDels) for breeding studies. Furthermore, studies regarding nutritional significance and health benefits are required to investigate the exact nutritional contents and health benefits of the brown-top millet. The present review delves into the nutritional value and health advantages of brown-top millet, as supported by the available literature. The limitations of producing brown-top millet have been enumerated. We also cover the status of marker-assisted breeding and functional genomics research on closely related species. Lastly, we draw insights for further research such as developing omics resources and applying genome editing to study and improve brown-top millet. This review will help to start breeding and other molecular studies to increase the growth and development of this cereal.
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Affiliation(s)
- P Bhavani
- Department of Biotechnology, University of Agricultural Sciences, Bangalore, Karnataka, India.
| | - C Nandini
- Zonal Agricultural and Horticultural Research Station, Babbur Farm, Hiriyur, KSNUAHS, Shivamogga, Karnataka, India.
| | - Theivanayagam Maharajan
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, 683104, Kerala, India
| | - T M Ningaraju
- Department of Biotechnology, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - B Nandini
- College of Horticulture, Kolar, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - S Gazala Parveen
- AICRP on Small Millets, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India
| | - K Pushpa
- Department of Agronomy, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India
| | - R L Ravikumar
- Department of Biotechnology, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - T E Nagaraja
- AICRP on Small Millets, University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India
| | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, 683104, Kerala, India
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13
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Kapoor C, Anamika, Mukesh Sankar S, Singh SP, Singh N, Kumar S. Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet. PLANTA 2024; 259:155. [PMID: 38750378 DOI: 10.1007/s00425-024-04423-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION Pearl 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.
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Affiliation(s)
- Chandan Kapoor
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Anamika
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Mukesh Sankar
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - S P Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nirupma Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sudhir Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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14
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Yong WCM, Devi A, Lin TF, Chappell HF. First principles modelling of the ion binding capacity of finger millet. NPJ Sci Food 2024; 8:28. [PMID: 38744951 PMCID: PMC11094100 DOI: 10.1038/s41538-024-00270-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Finger millet, a cereal grain widely consumed in India and Africa, has gained more attention in recent years due to its high dietary fibre (arabinoxylan) and trace mineral content, and its climate resilience. The aim of this study was to understand the interactions between potassium (K+), calcium (Ca2+) and zinc (Zn2+) ions and the arabinoxylan structure and determine its ion-binding capacity. Three variations of a proposed model of the arabinoxylan structure were constructed and first principles Density Functional Theory calculations were carried out to determine the cation-binding capacity of the arabinoxylan complexes. Zn2+-arabinoxylan complexes were highly unstable and thermodynamically unfavourable in all three models. Ca2+ and K+ ions, however, form thermodynamically stable complexes, particularly involving two glucuronic acid residues as a binding pocket. Glucuronic acid residues are found to play a key role in stabilising the cation-arabinoxylan complex, and steric effects are more important to the stability than charge density. Our results highlight the most important structural features of the millet fibre regarding ion-storage capacity, and provide valuable preliminary data for confirmatory experimental studies and for the planning of clinical trials where the bioavailability of bound ions following digestion may be tested.
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Affiliation(s)
| | - Apramita Devi
- Department of Viticulture and Enology, University of California, Davis, CA, USA
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Tsair-Fuh Lin
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Helen F Chappell
- School of Food Science and Nutrition, University of Leeds, Leeds, UK.
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15
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Prusty A, Panchal A, Singh RK, Prasad M. Major transcription factor families at the nexus of regulating abiotic stress response in millets: a comprehensive review. PLANTA 2024; 259:118. [PMID: 38592589 DOI: 10.1007/s00425-024-04394-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/17/2024] [Indexed: 04/10/2024]
Abstract
Millets stand out as a sustainable crop with the potential to address the issues of food insecurity and malnutrition. These small-seeded, drought-resistant cereals have adapted to survive a broad spectrum of abiotic stresses. Researchers are keen on unravelling the regulatory mechanisms that empower millets to withstand environmental adversities. The aim is to leverage these identified genetic determinants from millets for enhancing the stress tolerance of major cereal crops through genetic engineering or breeding. This review sheds light on transcription factors (TFs) that govern diverse abiotic stress responses and play role in conferring tolerance to various abiotic stresses in millets. Specifically, the molecular functions and expression patterns of investigated TFs from various families, including bHLH, bZIP, DREB, HSF, MYB, NAC, NF-Y and WRKY, are comprehensively discussed. It also explores the potential of TFs in developing stress-tolerant crops, presenting a comprehensive discussion on diverse strategies for their integration.
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Affiliation(s)
- Ankita Prusty
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Panchal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Roshan Kumar Singh
- Department of Botany, Mahishadal Raj College, Purba Medinipur, Garh Kamalpur, West Bengal, 721628, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Department of Genetics, University of Delhi, South Campus, Benito-Juarez Road, New Delhi, 110021, India.
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16
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Lou X, Gupta SK, Takano T, Tsugama D. Data of RNA sequencing of pearl millet panicles treated with a high temperature. Data Brief 2024; 53:110074. [PMID: 38312989 PMCID: PMC10837489 DOI: 10.1016/j.dib.2024.110074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 02/06/2024] Open
Abstract
Pearl millet (Pennisetum glaucum) is a cereal crop that can grow and set seeds even under drought, high temperatures and nutrient-poor conditions. Panicles of two pearl millet cultivars that differ in seed-setting rates were exposed to two different high-temperature treatments at three different developmental stages with three replicates, and RNA was prepared from these panicles. The resulting RNA samples were subjected to sequencing with the Illumina NovaSeq 6000 sequencer. The obtained data were 150-base-paired-end reads and were approximately 5 Gb/sample in total. These read data were deposited as those for a project in the NCBI (National Center for Biotechnology Information) BioProject database.
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Affiliation(s)
- Xichao Lou
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo 188-0002, Japan
| | - Shashi Kumar Gupta
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324, India
| | - Tetsuo Takano
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo 188-0002, Japan
| | - Daisuke Tsugama
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo 188-0002, Japan
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17
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Thudi M, Samineni S, Li W, Boer MP, Roorkiwal M, Yang Z, Ladejobi F, Zheng C, Chitikineni A, Nayak S, He Z, Valluri V, Bajaj P, Khan AW, Gaur PM, van Eeuwijk F, Mott R, Xin L, Varshney RK. Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea. THE PLANT GENOME 2024; 17:e20333. [PMID: 37122200 DOI: 10.1002/tpg2.20333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/17/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Terminal drought is one of the major constraints to crop production in chickpea (Cicer arietinum L.). In order to map drought tolerance related traits at high resolution, we sequenced multi-parent advanced generation intercross (MAGIC) population using whole genome resequencing approach and phenotyped it under drought stress environments for two consecutive years (2013-14 and 2014-15). A total of 52.02 billion clean reads containing 4.67 TB clean data were generated on the 1136 MAGIC lines and eight parental lines. Alignment of clean data on to the reference genome enabled identification of a total, 932,172 of SNPs, 35,973 insertions, and 35,726 deletions among the parental lines. A high-density genetic map was constructed using 57,180 SNPs spanning a map distance of 1606.69 cM. Using compressed mixed linear model, genome-wide association study (GWAS) enabled us to identify 737 markers significantly associated with days to 50% flowering, days to maturity, plant height, 100 seed weight, biomass, and harvest index. In addition to the GWAS approach, an identity-by-descent (IBD)-based mixed model approach was used to map quantitative trait loci (QTLs). The IBD-based mixed model approach detected major QTLs that were comparable to those from the GWAS analysis as well as some exclusive QTLs with smaller effects. The candidate genes like FRIGIDA and CaTIFY4b can be used for enhancing drought tolerance in chickpea. The genomic resources, genetic map, marker-trait associations, and QTLs identified in the study are valuable resources for the chickpea community for developing climate resilient chickpeas.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, India
| | - Srinivasan Samineni
- Crop Improvement Program-Asia, ICRISAT, Patancheru, India
- International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Wenhao Li
- Wageningen University and Research, Wageningen, The Netherlands
| | - Martin P Boer
- Wageningen University and Research, Wageningen, The Netherlands
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University, Al Ain, United Arab Emirates
| | | | - Funmi Ladejobi
- Department of Genetics, Evolution and Environment, Genetics Institute, University College London, London, UK
| | - Chaozhi Zheng
- Wageningen University and Research, Wageningen, The Netherlands
- BGI-Shenzhen, Shenzhen, China
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sourav Nayak
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Vinod Valluri
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Aamir W Khan
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Pooran M Gaur
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, India
- The UWA Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | | | - Richard Mott
- Department of Genetics, Evolution and Environment, Genetics Institute, University College London, London, UK
| | - Liu Xin
- BGI-Shenzhen, Shenzhen, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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18
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Jha DK, Chanwala J, Barla P, Dey N. "Genome-wide identification of bZIP gene family in Pearl millet and transcriptional profiling under abiotic stress, phytohormonal treatments; and functional characterization of PgbZIP9". FRONTIERS IN PLANT SCIENCE 2024; 15:1352040. [PMID: 38469329 PMCID: PMC10925649 DOI: 10.3389/fpls.2024.1352040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024]
Abstract
Abiotic stresses are major constraints in crop production, and are accountable for more than half of the total crop loss. Plants overcome these environmental stresses using coordinated activities of transcription factors and phytohormones. Pearl millet an important C4 cereal plant having high nutritional value and climate resilient features is grown in marginal lands of Africa and South-East Asia including India. Among several transcription factors, the basic leucine zipper (bZIP) is an important TF family associated with diverse biological functions in plants. In this study, we have identified 98 bZIP family members (PgbZIP) in pearl millet. Phylogenetic analysis divided these PgbZIP genes into twelve groups (A-I, S, U and X). Motif analysis has shown that all the PgbZIP proteins possess conserved bZIP domains and the exon-intron organization revealed conserved structural features among the identified genes. Cis-element analysis, RNA-seq data analysis, and real-time expression analysis of PgbZIP genes suggested the potential role of selected PgbZIP genes in growth/development and abiotic stress responses in pearl millet. Expression profiling of selected PgbZIPs under various phytohormones (ABA, SA and MeJA) treatment showed differential expression patterns of PgbZIP genes. Further, PgbZIP9, a homolog of AtABI5 was found to localize in the nucleus and modulate gene expression in pearl millet under stresses. Our present findings provide a better understanding of bZIP genes in pearl millet and lay a good foundation for the further functional characterization of multi-stress tolerant PgbZIP genes, which could become efficient tools for crop improvement.
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Affiliation(s)
- Deepak Kumar Jha
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Jeky Chanwala
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Preeti Barla
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
| | - Nrisingha Dey
- Division of Plant and Microbial Biotechnology, Institute of Life Sciences, Bhubaneswar, India
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19
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Kandarkar K, Palaniappan V, Satpathy S, Vemula A, Rajasekaran R, Jeyakumar P, Sevugaperumal N, Gupta SK. Understanding genetic diversity in drought-adaptive hybrid parental lines in pearl millet. PLoS One 2024; 19:e0298636. [PMID: 38394324 PMCID: PMC10890771 DOI: 10.1371/journal.pone.0298636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Information on genetic diversity and population structure is helpful to strategize enhancing the genetic base of hybrid parental lines in breeding programs. The present study determined the population structure and genetic diversity of 109 pearl millet hybrid parental lines, known for their better adaptation and performance in drought-prone environments, using 16,472 single nucleotide polymorphic (SNP) markers generated from GBS (genotyping-by-sequencing) platforms. The SNPs were distributed uniformly across the pearl millet genome and showed considerable genetic diversity (0.337), expected heterozygosity (0.334), and observed heterozygosity (0.031). Most of the pairs of lines (78.36%) had Identity-by-State (IBS) based genetic distances of more than 0.3, indicating a significant amount of genetic diversity among the parental lines. Bayesian model-based population stratification, neighbor-joining phylogenetic analysis, and principal coordinate analysis (PCoA) differentiated all hybrid parental lines into two clear-cut major groups, one each for seed parents (B-lines) and pollinators (R-lines). Majority of parental lines sharing common parentages were found grouped in the same cluster. Analysis of molecular variance (AMOVA) revealed 7% of the variation among subpopulations, and 93% of the variation was attributable to within sub-populations. Chromosome 3 had the highest number of LD regions. Genomic LD decay distance was 0.69 Mb and varied across the different chromosomes. Genetic diversity based on 11 agro-morphological and grain quality traits also suggested that the majority of the B- and R-lines were grouped into two major clusters with few overlaps. In addition, the combined analysis of phenotypic and genotypic data showed similarities in the population grouping patterns. The present study revealed the uniqueness of most of the inbred lines, which can be a valuable source of new alleles and help breeders to utilize these inbred lines for the development of hybrids in drought-prone environments.
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Affiliation(s)
- Kuldeep Kandarkar
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Viswanathan Palaniappan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Subhrajit Satpathy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Anilkumar Vemula
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Ravikesavan Rajasekaran
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Prabhakaran Jeyakumar
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Nakkeeran Sevugaperumal
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Shashi Kumar Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
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20
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Xu L, Lan Y, Lin M, Zhou H, Ying S, Chen M. Genome-Wide Identification and Transcriptional Analysis of AP2/ERF Gene Family in Pearl Millet ( Pennisetum glaucum). Int J Mol Sci 2024; 25:2470. [PMID: 38473718 DOI: 10.3390/ijms25052470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The apetala2/ethylene response factor (AP2/ERF) gene family plays a crucial role in regulating plant growth and development and responding to different abiotic stresses (e.g., drought, heat, cold, and salinity). However, the knowledge of the ERF family in pearl millet remains limited. Here, a total of 167 high-confidence PgERF genes are identified and divided into five subgroups based on gene-conserved structure and phylogenetic analysis. Forty-one pairs of segmental duplication are found using collinear analysis. Nucleotide substitution analysis reveals these duplicated pairs are under positive purification, indicating they are actively responding to natural selection. Comprehensive transcriptomic analysis reveals that PgERF genesare preferentially expressed in the imbibed seeds and stem (tilling stage) and respond to heat, drought, and salt stress. Prediction of the cis-regulatory element by the PlantCARE program indicates that PgERF genes are involved in responses to environmental stimuli. Using reverse transcription quantitative real-time PCR (RT-qPCR), expression profiles of eleven selected PgERF genes are monitored in various tissues and during different abiotic stresses. Transcript levels of each PgERF gene exhibit significant changes during stress treatments. Notably, the PgERF7 gene is the only candidate that can be induced by all adverse conditions. Furthermore, four PgERF genes (i.e., PgERF22, PgERF37, PgERF88, and PgERF155) are shown to be involved in the ABA-dependent signaling pathway. These results provide useful bioinformatic and transcriptional information for understanding the roles of the pearl millet ERF gene family in adaptation to climate change.
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Affiliation(s)
- Liang Xu
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Ying Lan
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Miaohong Lin
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Hongkai Zhou
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
| | - Sheng Ying
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Miao Chen
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524091, China
- Shenzhen Institute, Guangdong Ocean University, Shenzhen 518120, China
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21
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de la Fuente C, Grondin A, Sine B, Debieu M, Belin C, Hajjarpoor A, Atkinson JA, Passot S, Salson M, Orjuela J, Tranchant-Dubreuil C, Brossier JR, Steffen M, Morgado C, Dinh HN, Pandey BK, Darmau J, Champion A, Petitot AS, Barrachina C, Pratlong M, Mounier T, Nakombo-Gbassault P, Gantet P, Gangashetty P, Guedon Y, Vadez V, Reichheld JP, Bennett MJ, Kane NA, Guyomarc'h S, Wells DM, Vigouroux Y, Laplaze L. Glutaredoxin regulation of primary root growth is associated with early drought stress tolerance in pearl millet. eLife 2024; 12:RP86169. [PMID: 38294329 PMCID: PMC10945517 DOI: 10.7554/elife.86169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet's early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modeling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including genome-wide association study and quantitative trait loci (QTL) approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re-annotation of one of these genomic regions identified a glutaredoxin-encoding gene PgGRXC9 as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homolog AtROXY19 revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment.
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Affiliation(s)
| | - Alexandre Grondin
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
- LMI LAPSEDakarSenegal
- CERAAS, ISRAThiesSenegal
| | | | - Marilyne Debieu
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | | | - Amir Hajjarpoor
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Jonathan A Atkinson
- School of Biosciences, University of NottinghamSutton BoningtonUnited Kingdom
| | - Sixtine Passot
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Marine Salson
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Julie Orjuela
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | | | | | - Maxime Steffen
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | | | - Hang Ngan Dinh
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Bipin K Pandey
- School of Biosciences, University of NottinghamSutton BoningtonUnited Kingdom
| | - Julie Darmau
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Antony Champion
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | | | | | | | | | | | - Pascal Gantet
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | | | - Yann Guedon
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Vincent Vadez
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
- LMI LAPSEDakarSenegal
- CERAAS, ISRAThiesSenegal
| | | | - Malcolm J Bennett
- School of Biosciences, University of NottinghamSutton BoningtonUnited Kingdom
| | | | | | - Darren M Wells
- School of Biosciences, University of NottinghamSutton BoningtonUnited Kingdom
| | - Yves Vigouroux
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
| | - Laurent Laplaze
- DIADE, Université de Montpellier, IRD, CIRADMontpellierFrance
- LMI LAPSEDakarSenegal
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22
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Alahmad A, Harir M, Fochesato S, Tulumello J, Walker A, Barakat M, Ndour PMS, Schmitt-Kopplin P, Cournac L, Laplaze L, Heulin T, Achouak W. Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet. MICROBIOME 2024; 12:1. [PMID: 38167150 PMCID: PMC10763007 DOI: 10.1186/s40168-023-01727-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/19/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, and rhizosheath structure in pearl millet using four distinct lines with contrasting soil aggregation abilities. RESULTS Utilizing 16S rRNA gene and ITS metabarcoding for microbiota profiling, coupled with FTICR-MS metabonomic analysis of metabolite composition in distinct plant compartments and root exudates, we revealed substantial disparities in microbial diversity and interaction networks. The ß-NTI analysis highlighted bacterial rhizosphere turnover driven primarily by deterministic processes, showcasing prevalent homogeneous selection in root tissue (RT) and root-adhering soil (RAS). Conversely, fungal communities were more influenced by stochastic processes. In bulk soil assembly, a combination of deterministic and stochastic mechanisms shapes composition, with deterministic factors exerting a more pronounced role. Metabolic profiles across shoots, RT, and RAS in different pearl millet lines mirrored their soil aggregation levels, emphasizing the impact of inherent plant traits on microbiota composition and unique metabolic profiles in RT and exudates. Notably, exclusive presence of antimicrobial compounds, including DIMBOA and H-DIMBOA, emerged in root exudates and RT of low aggregation lines. CONCLUSIONS This research underscores the pivotal influence of root exudates in shaping the root-associated microbiota composition across pearl millet lines, entwined with their soil aggregation capacities. These findings underscore the interconnectedness of root exudates and microbiota, which jointly shape rhizosheath structure, deepening insights into soil-plant-microbe interactions and ecological processes shaping rhizosphere microbial communities. Deciphering plant-microbe interactions and their contribution to soil aggregation and microbiota dynamics holds promise for the advancement of sustainable agricultural strategies. Video Abstract.
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Affiliation(s)
- Abdelrahman Alahmad
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
- UniLaSalle, SFR NORVEGE FED 4277, AGHYLE Rouen UP 2018.C101, 3 Rue du Tronquet, 76130, Mont-Saint- Aignan, France
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- Chair Analytl Food Chem, Technical University of Munich, 85354, Freising, Weihenstephan, Germany
| | - Sylvain Fochesato
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Joris Tulumello
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Mohamed Barakat
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Papa Mamadou Sitor Ndour
- CIRAD, INRAE, Eco&Sols, Université de Montpellier, Institut Agro, IRD FR, Montpellier, France
- UCEIV-ULCO, 50 Rue Ferdinand Buisson, 62228, Calais, France
- LMI IESOL, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- Chair Analytl Food Chem, Technical University of Munich, 85354, Freising, Weihenstephan, Germany
| | - Laurent Cournac
- CIRAD, INRAE, Eco&Sols, Université de Montpellier, Institut Agro, IRD FR, Montpellier, France
- LMI IESOL, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Laurent Laplaze
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LMI LAPSE, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Thierry Heulin
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France.
| | - Wafa Achouak
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France.
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23
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Wang X, Tu M, Wang Y, Zhang Y, Yin W, Fang J, Gao M, Li Z, Zhan W, Fang Y, Song J, Xi Z, Wang X. Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics. HORTICULTURE RESEARCH 2024; 11:uhad260. [PMID: 38288254 PMCID: PMC10822838 DOI: 10.1093/hr/uhad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/26/2023] [Indexed: 01/31/2024]
Abstract
Grapes are globally recognized as economically significant fruit trees. Among grape varieties, Thompson Seedless holds paramount influence for fresh consumption and for extensive applications in winemaking, drying, and juicing. This variety is one of the most efficient genotypes for grape genetic modification. However, the lack of a high-quality genome has impeded effective breeding efforts. Here, we present the high-quality reference genome of Thompson Seedless with all 19 chromosomes represented as 19 contiguous sequences (N50 = 27.1 Mb) with zero gaps and prediction of all telomeres and centromeres. Compared with the previous assembly (TSv1 version), the new assembly incorporates an additional 31.5 Mb of high-quality sequenced data with annotation of a total of 30 397 protein-coding genes. We also performed a meticulous analysis to identify nucleotide-binding leucine-rich repeat genes (NLRs) in Thompson Seedless and two wild grape varieties renowned for their disease resistance. Our analysis revealed a significant reduction in the number of two types of NLRs, TIR-NB-LRR (TNL) and CC-NB-LRR (CNL), in Thompson Seedless, which may have led to its sensitivity to many fungal diseases, such as powdery mildew, and an increase in the number of a third type, RPW8 (resistance to powdery mildew 8)-NB-LRR (RNL). Subsequently, transcriptome analysis showed significant enrichment of NLRs during powdery mildew infection, emphasizing the pivotal role of these elements in grapevine's defense against powdery mildew. The successful assembly of a high-quality Thompson Seedless reference genome significantly contributes to grape genomics research, providing insight into the importance of seedlessness, disease resistance, and color traits, and these data can be used to facilitate grape molecular breeding efforts.
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Affiliation(s)
- Xianhang Wang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxing Tu
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ya Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yali Zhang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wuchen Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinghao Fang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Min Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Zhan
- Xi'an Haorui Genomics Technology Co., Ltd, Xi'an 710116, China
| | - Yulin Fang
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junyang Song
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhumei Xi
- College of Enology, College of Food Science and Engineering, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Shaanxi Engineering Research Center for Viti-Viniculture, Heyang Viti-Viniculture Station, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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24
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Wei M, Liu J, Wang S, Wang X, Liu H, Ma Q, Wang J, Shi W. Genetic Diversity and Phylogenetic Analysis of Zygophyllum loczyi in Northwest China's Deserts Based on the Resequencing of the Genome. Genes (Basel) 2023; 14:2152. [PMID: 38136974 PMCID: PMC10742952 DOI: 10.3390/genes14122152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
In order to study the genetics of local adaptation in all main deserts of northwest China, whole genomes of 169 individuals were resequenced, which covers 20 populations of Zygophyllum loczyi (Zygophyllales: Zygophylaceae). We describe more than 15 million single nucleotide polymorphisms and numerous InDels. The expected heterozygosity and PIC values associated with local adaptation varied significantly across biogeographic regions. Variation in environmental factors contributes largely to the population genetic structure of Z. loczyi. Bayesian analysis performed with STRUCTURE defined four genetic clusters, while the results of principle component analysis were similar. Our results shows that the Qaidam Desert group appears to be diverging into two branches characterized by significant geographic separation and gene flow with two neighboring deserts. Geological data assume that it is possible that the Taklamakan Desert was the original distribution site, and Z. loczyi could have migrated later on and expanded within other desert areas. The above findings provide insights into the processes involved in biogeography, phylogeny, and differentiation within the northwest deserts of China.
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Affiliation(s)
- Mengmeng Wei
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingdian Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Suoming Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Xiyong Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
| | - Haisuang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Qing Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; (S.W.); (H.L.); (Q.M.)
| | - Jiancheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable, Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China; (M.W.); (J.L.); (X.W.); (J.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
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25
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Sun M, Yan H, Zhang A, Jin Y, Lin C, Luo L, Wu B, Fan Y, Tian S, Cao X, Wang Z, Luo J, Yang Y, Jia J, Zhou P, Tang Q, Jones CS, Varshney RK, Srivastava RK, He M, Xie Z, Wang X, Feng G, Nie G, Huang D, Zhang X, Zhu F, Huang L. Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2348-2357. [PMID: 37530223 PMCID: PMC10579705 DOI: 10.1111/pbi.14136] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/01/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023]
Abstract
Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.
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Affiliation(s)
- Min Sun
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Haidong Yan
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- School of Plant and Environmental SciencesVirginia TechBlacksburgVirginiaUSA
- Department of GeneticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Aling Zhang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yarong Jin
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Chuang Lin
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Lin Luo
- College of Life SciencesFujian Agriculture and Forestry UniversityFujianChina
| | - Bingchao Wu
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yuhang Fan
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Shilin Tian
- Novogene Bioinformatics InstituteBeijingChina
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life SciencesWuhan UniversityWuhanChina
| | | | - Zan Wang
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Jinchan Luo
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yuchen Yang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jiyuan Jia
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Puding Zhou
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Qianzi Tang
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Chris Stephen Jones
- Feed and Forage DevelopmentInternational Livestock Research InstituteNairobiKenya
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
- Murdoch's Centre for Crop and Food Innovation, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rakesh K. Srivastava
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduSichuanChina
| | - Zheni Xie
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- College of Agro‐Grassland ScienceNanjing Agricultural UniversityNanjingChina
| | - Xiaoshan Wang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Guangyan Feng
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Gang Nie
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Dejun Huang
- Herbivorous Livestock Research InstituteChongqing Academy of Animal SciencesChongqingChina
| | - Xinquan Zhang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Fangjie Zhu
- College of Life SciencesFujian Agriculture and Forestry UniversityFujianChina
| | - Linkai Huang
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduSichuanChina
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26
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Verbeecke V, Custódio L, Strobbe S, Van Der Straeten D. The role of orphan crops in the transition to nutritional quality-oriented crop improvement. Biotechnol Adv 2023; 68:108242. [PMID: 37640278 DOI: 10.1016/j.biotechadv.2023.108242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/09/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Micronutrient malnutrition is a persisting problem threatening global human health. Biofortification via metabolic engineering has been proposed as a cost-effective and short-term means to alleviate this burden. There has been a recent rise in the recognition of potential that underutilized, orphan crops can hold in decreasing malnutrition concerns. Here, we illustrate how orphan crops can serve as a medium to provide micronutrients to populations in need, whilst promoting and maintaining dietary diversity. We provide a roadmap, illustrating which aspects to be taken into consideration when evaluating orphan crops. Recent developments have shown successful biofortification via metabolic engineering in staple crops. This review provides guidance in the implementation of these successes to relevant orphan crop species, with a specific focus on the relevant micronutrients iron, zinc, provitamin A and folates.
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Affiliation(s)
- Vincent Verbeecke
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Laura Custódio
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Simon Strobbe
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.
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Kitashova A, Brodsky V, Chaturvedi P, Pierides I, Ghatak A, Weckwerth W, Nägele T. Quantifying the impact of dynamic plant-environment interactions on metabolic regulation. JOURNAL OF PLANT PHYSIOLOGY 2023; 290:154116. [PMID: 37839392 DOI: 10.1016/j.jplph.2023.154116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
A plant's genome encodes enzymes, transporters and many other proteins which constitute metabolism. Interactions of plants with their environment shape their growth, development and resilience towards adverse conditions. Although genome sequencing technologies and applications have experienced triumphantly rapid development during the last decades, enabling nowadays a fast and cheap sequencing of full genomes, prediction of metabolic phenotypes from genotype × environment interactions remains, at best, very incomplete. The main reasons are a lack of understanding of how different levels of molecular organisation depend on each other, and how they are constituted and expressed within a setup of growth conditions. Phenotypic plasticity, e.g., of the genetic model plant Arabidopsis thaliana, has provided important insights into plant-environment interactions and the resulting genotype x phenotype relationships. Here, we summarize previous and current findings about plant development in a changing environment and how this might be shaped and reflected in metabolism and its regulation. We identify current challenges in the study of plant development and metabolic regulation and provide an outlook of how methodological workflows might support the application of findings made in model systems to crops and their cultivation.
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Affiliation(s)
- Anastasia Kitashova
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Vladimir Brodsky
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Palak Chaturvedi
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Iro Pierides
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Arindam Ghatak
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Wolfram Weckwerth
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Thomas Nägele
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
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Narayanrao DR, Tomar RS, Sm P, Jasminkumar K, Ashish G, Chauhan NM, Singh SC, Upadhye V, Kuddus M, Kamble L, Hajare ST. De novo transcriptome sequencing of drought tolerance-associated genes in little millet (Panicum sumatrense L.). Funct Integr Genomics 2023; 23:303. [PMID: 37723408 DOI: 10.1007/s10142-023-01221-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 09/20/2023]
Abstract
The genome size of the little millet Panicum sumatrense is unknown, although its genome is fairly diploid (2n = 4x = 36). Despite tremendous nutritional value and adaptability to adverse climatic conditions, P. sumatrense use was limited by their low palatability, coarse grain, and lack of variety of culinary preparations. Hence, understanding how to vary their usage to offer food and nutritional security in the continuously changing modern world, the proposed study was aimed to determine potential genes and metabolites implicated in drought resistance. The drought-resistant genotype of tiny millet OLM-203/Tarini was offered in pots under both relaxed and demanding circumstances. The experimental seedlings were 32 days old and had been under water stress for 23 days. A total of 7606 genes were compared between 23 and 32 days for roots and 7264 total genes were compared between 23 and 32 days for leaves, according to a research on differential expression genes (DEGs). Twenty essential genes for drought tolerance were up-or down-regulated in the control and treated roots of the OLM-203 genotype. For instance, the genes RS193 and XB34 were up-regulated in leaves while, WLIM1 was found to be down-regulated. Gene SKI35 was up-regulated in roots, whereas MPK6 and TCMOp1 were down-regulated in root samples. The roots and leaves of the tiny millet OLM-203 genotype expressed 36 up-regulated and 21 down-regulated serine transcripts, respectively. Gene annotations for leaf samples were classified as having "molecular function" (46%), "cellular component" (19%), and "biological process" (35%), while root sample gene annotations were categorized as having "biological process" (573 contigs), "molecular function" (401 contigs), and "cellular components" (166 contigs). Noteworthy, polyamines play a crucial role in drought stress tolerance in the genotype, and it was found that top ten DEGs encoding for polyamines were common in two tissues (leaf and root). Collectively, transcriptomics profiling (RNA-seq) unveiled transcriptional stability drought stress provide a new insight in underlying modus of operandi in little millet genotype "OLM-203/Tarini" in response to heat stress.
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Affiliation(s)
| | - R S Tomar
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Padhiyar Sm
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Kheni Jasminkumar
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Gulwe Ashish
- Department of Bioinformatics, Sub Campus Latur, Swami Ramanand Teerth Marathawada University, Nanded, India
| | - Nitin Mahendra Chauhan
- ILRI and College of Natural and Computational Sciences, Dilla University, 419, Dilla, Ethiopia
| | | | - Vijay Upadhye
- Research and Development Cell (RDC), Parul Institute of Applied Sciences (PIAS), Parul University, Vadodara, India
| | - Mohammed Kuddus
- Department of Biochemistry, College of Medicine, University of Hail, Hail, Kingdom of Saudi Arabia
| | - Laxmikant Kamble
- Deputy Director and Associate Professor (CD4D), Parul University, Vadodara, Gujarat, India
- Swami Ramanand Teerth Marathawada University, Nanded, India
| | - Sunil Tulshiram Hajare
- ILRI and College of Natural and Computational Sciences, Dilla University, 419, Dilla, Ethiopia.
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Zheng H, Wang B, Hua X, Gao R, Wang Y, Zhang Z, Zhang Y, Mei J, Huang Y, Huang Y, Lin H, Zhang X, Lin D, Lan S, Liu Z, Lu G, Wang Z, Ming R, Zhang J, Lin Z. A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis. PLANT COMMUNICATIONS 2023; 4:100633. [PMID: 37271992 PMCID: PMC10504591 DOI: 10.1016/j.xplc.2023.100633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/07/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
JUJUNCAO (Cenchrus fungigraminus; 2n = 4x = 28) is a Cenchrus grass with the highest biomass production among cultivated plants, and it can be used for mushroom cultivation, animal feed, and biofuel production. Here, we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated ∼2.7 million years ago (mya). Its genome consists of two subgenomes, and subgenome A shares high collinear synteny with pearl millet. We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO. Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes, which was a further indication of asymmetric DNA methylation. The three types of centromeric repeat in the JUJUNCAO genome (CEN137, CEN148, and CEN156) may have evolved independently within each subgenome, with some introgressions of CEN156 from the B to the A subgenome. We investigated the photosynthetic characteristics of JUJUNCAO, revealing its typical C4 Kranz anatomy and high photosynthetic efficiency. NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO, which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield. Taken together, our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies, as well as genetic improvement of Cenchrus grasses.
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Affiliation(s)
- Huakun Zheng
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baiyu Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, Guangxi, China; Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiuting Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, Guangxi, China
| | - Ruiting Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yuhao Wang
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zixin Zhang
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yixing Zhang
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Mei
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongji Huang
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Yumin Huang
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hui Lin
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xingtan Zhang
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongmei Lin
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongjian Liu
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guodong Lu
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ray Ming
- Center for Genomics, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, Guangxi, China.
| | - Zhanxi Lin
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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30
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Chaudhary N, Salgotra RK, Chauhan BS. Genetic Enhancement of Cereals Using Genomic Resources for Nutritional Food Security. Genes (Basel) 2023; 14:1770. [PMID: 37761910 PMCID: PMC10530810 DOI: 10.3390/genes14091770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Advances in genomics resources have facilitated the evolution of cereal crops with enhanced yield, improved nutritional values, and heightened resistance to various biotic and abiotic stresses. Genomic approaches present a promising avenue for the development of high-yielding varieties, thereby ensuring food and nutritional security. Significant improvements have been made within the omics domain, specifically in genomics, transcriptomics, and proteomics. The advent of Next-Generation Sequencing (NGS) techniques has yielded an immense volume of data, accompanied by substantial progress in bioinformatic tools for proficient analysis. The synergy between genomics and computational tools has been acknowledged as pivotal for unravelling the intricate mechanisms governing genome-wide gene regulation. Within this review, the essential genomic resources are delineated, and their harmonization in the enhancement of cereal crop varieties is expounded upon, with a paramount focus on fulfilling the nutritional requisites of humankind. Furthermore, an encompassing compendium of the available genomic resources for cereal crops is presented, accompanied by an elucidation of their judicious utilization in the advancement of crop attributes.
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Affiliation(s)
- Neeraj Chaudhary
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180009, Jammu and Kashmir, India; (N.C.); (R.K.S.)
| | - Romesh Kumar Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180009, Jammu and Kashmir, India; (N.C.); (R.K.S.)
| | - Bhagirath Singh Chauhan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Gatton, QLD 4343, Australia
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Ramu P, Srivastava RK, Sanyal A, Fengler K, Cao J, Zhang Y, Nimkar M, Gerke J, Shreedharan S, Llaca V, May G, Peterson-Burch B, Lin H, King M, Das S, Bhupesh V, Mandaokar A, Maruthachalam K, Krishnamurthy P, Gandhi H, Rathore A, Gupta R, Chitikineni A, Bajaj P, Gupta SK, Satyavathi CT, Pandravada A, Varshney RK, Babu R. Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications. Commun Biol 2023; 6:902. [PMID: 37667032 PMCID: PMC10477261 DOI: 10.1038/s42003-023-05258-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023] Open
Abstract
High-quality reference genome assemblies, representative of global heterotic patterns, offer an ideal platform to accurately characterize and utilize genetic variation in the primary gene pool of hybrid crops. Here we report three platinum grade de-novo, near gap-free, chromosome-level reference genome assemblies from the active breeding germplasm in pearl millet with a high degree of contiguity, completeness, and accuracy. An improved Tift genome (Tift23D2B1-P1-P5) assembly has a contig N50 ~ 7,000-fold (126 Mb) compared to the previous version and better alignment in centromeric regions. Comparative genome analyses of these three lines clearly demonstrate a high level of collinearity and multiple structural variations, including inversions greater than 1 Mb. Differential genes in improved Tift genome are enriched for serine O-acetyltransferase and glycerol-3-phosphate metabolic process which play an important role in improving the nutritional quality of seed protein and disease resistance in plants, respectively. Multiple marker-trait associations are identified for a range of agronomic traits, including grain yield through genome-wide association study. Improved genome assemblies and marker resources developed in this study provide a comprehensive framework/platform for future applications such as marker-assisted selection of mono/oligogenic traits as well as whole-genome prediction and haplotype-based breeding of complex traits.
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Affiliation(s)
- Punna Ramu
- Corteva Agriscience, Hyderabad, Telangana, India
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India.
| | | | | | - Jun Cao
- Corteva Agriscience, Johnston, IA, 50131, USA
| | - Yun Zhang
- Corteva Agriscience, Johnston, IA, 50131, USA
| | | | | | | | | | - Gregory May
- Corteva Agriscience, Johnston, IA, 50131, USA
| | | | - Haining Lin
- Corteva Agriscience, Johnston, IA, 50131, USA
- Moderna, 200 Technology Square, Cambridge, MA, 02139, USA
| | - Matthew King
- Corteva Agriscience, Johnston, IA, 50131, USA
- Natera Inc, San Carlos, CA, 94070, USA
| | - Sayan Das
- Corteva Agriscience, Hyderabad, Telangana, India
| | - Vaid Bhupesh
- Corteva Agriscience, Hyderabad, Telangana, India
| | | | | | | | - Harish Gandhi
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
- International Maize and Wheat Improvement Center (CIMMYT), Hyderabad, India
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Prasad Bajaj
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - S K Gupta
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - C Tara Satyavathi
- Indian Council of Agricultural Research - All India Coordinated Research Project on Pearl Millet, Jodhpur, India
| | | | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India.
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Raman Babu
- Corteva Agriscience, Hyderabad, Telangana, India.
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32
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Teng K, Guo Q, Liu L, Guo Y, Xu Y, Hou X, Teng W, Zhang H, Zhao C, Yue Y, Wen H, Wu J, Fan X. Chromosome-level reference genome assembly provides insights into the evolution of Pennisetum alopecuroides. FRONTIERS IN PLANT SCIENCE 2023; 14:1195479. [PMID: 37680353 PMCID: PMC10481962 DOI: 10.3389/fpls.2023.1195479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/28/2023] [Indexed: 09/09/2023]
Abstract
Pennisetum alopecuroides is an important forage grass resource, which plays a vital role in ecological environment improvement. Therefore, the acquisition of P. alopecuroides genome resources is conducive to the study of the adaptability of Pennisetum species in ecological remediation and forage breeding development. Here we assembled a P. alopecuroides cv. 'Liqiu' genome at the chromosome level with a size of approximately 845.71 Mb, contig N50 of 84.83Mb, and genome integrity of 99.13% as assessed by CEGMA. A total of 833.41-Mb sequences were mounted on nine chromosomes by Hi-C technology. In total, 60.66% of the repetitive sequences and 34,312 genes were predicted. The genomic evolution analysis showed that P. alopecuroides cv. 'Liqiu' was isolated from Setaria 7.53-13.80 million years ago and from Cenchrus 5.33-8.99 million years ago, respectively. The whole-genome event analysis showed that P. alopecuroides cv. 'Liqiu' underwent two whole-genome duplication (WGD) events in the evolution process, and the duplication events occurred at a similar time to that of Oryza sativa and Setaria viridis. The completion of the genome sequencing of P. alopecuroides cv. 'Liqiu' provides data support for mining high-quality genetic resources of P. alopecuroides and provides a theoretical basis for the origin and evolutionary characteristics of Pennisetum.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yuesen Yue
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | | | | | - Xifeng Fan
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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33
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Varshney RK. Meet the PCP Editor-Rajeev K. Varshney FRS. PLANT & CELL PHYSIOLOGY 2023; 64:841-843. [PMID: 37338338 PMCID: PMC10434731 DOI: 10.1093/pcp/pcad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 06/21/2023]
Affiliation(s)
- Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA 6150, Australia
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34
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Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. MOLECULAR PLANT 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
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Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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Raza A, Bohra A, Varshney RK. Pan-genome for pearl millet that beats the heat. TRENDS IN PLANT SCIENCE 2023; 28:857-860. [PMID: 37173271 DOI: 10.1016/j.tplants.2023.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
A better understanding of crop genomes reveals that structural variations (SVs) are crucial for genetic improvement. A graph-based pan-genome by Yan et al. uncovered 424 085 genomic SVs and provided novel insights into heat tolerance of pearl millet. We discuss how these SVs can fast-track pearl millet breeding under harsh environments.
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Affiliation(s)
- Ali Raza
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Abhishek Bohra
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia.
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Xing L, Wang M, He Q, Zhang H, Liang H, Zhou Q, Liu Y, Liu Z, Wang Y, Du C, Xiao Y, Liu J, Li W, Liu G, Du H. Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum. BMC Biol 2023; 21:161. [PMID: 37480118 PMCID: PMC10362693 DOI: 10.1186/s12915-023-01643-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/06/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation. RESULTS Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum. CONCLUSIONS Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum.
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Affiliation(s)
- Longsheng Xing
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Meijia Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Qiang He
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Hongyu Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Hanfei Liang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Qinghong Zhou
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yu Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Ze Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yu Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Cailian Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yao Xiao
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Jianan Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Wei Li
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Guixia Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China.
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China.
| | - Huilong Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China.
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China.
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Rani V, Joshi DC, Joshi P, Singh R, Yadav D. "Millet Models" for harnessing nuclear factor-Y transcription factors to engineer stress tolerance in plants: current knowledge and emerging paradigms. PLANTA 2023; 258:29. [PMID: 37358736 DOI: 10.1007/s00425-023-04186-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
MAIN CONCLUSION The main purpose of this review is to shed light on the role of millet models in imparting climate resilience and nutritional security and to give a concrete perspective on how NF-Y transcription factors can be harnessed for making cereals more stress tolerant. Agriculture faces significant challenges from climate change, bargaining, population, elevated food prices, and compromises with nutritional value. These factors have globally compelled scientists, breeders, and nutritionists to think of some options that can combat the food security crisis and malnutrition. To address these challenges, mainstreaming the climate-resilient and nutritionally unparalleled alternative crops like millet is a key strategy. The C4 photosynthetic pathway and adaptation to low-input marginal agricultural systems make millets a powerhouse of important gene and transcription factor families imparting tolerance to various kinds of biotic and abiotic stresses. Among these, the nuclear factor-Y (NF-Y) is one of the prominent transcription factor families that regulate diverse genes imparting stress tolerance. The primary purpose of this article is to shed light on the role of millet models in imparting climate resilience and nutritional security and to give a concrete perspective on how NF-Y transcription factors can be harnessed for making cereals more stress tolerant. Future cropping systems could be more resilient to climate change and nutritional quality if these practices were implemented.
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Affiliation(s)
- Varsha Rani
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - D C Joshi
- ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, 263601, India
| | - Priyanka Joshi
- Plant and Environmental Sciences, 113 Biosystems Research Complex, Clemson University, Clemson, South Carolina, 29634, USA
| | - Rajesh Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Dinesh Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India.
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Pandey S, Singh A, Jaiswal P, Singh MK, Meena KR, Singh SK. The potentialities of omics resources for millet improvement. Funct Integr Genomics 2023; 23:210. [PMID: 37355501 DOI: 10.1007/s10142-023-01149-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Millets are nutrient-rich (nutri-rich) cereals with climate resilience attributes. However, its full productive potential is not realized due to the lack of a focused yield improvement approach, as evidenced by the available literature. Also, the lack of well-characterized genomic resources significantly limits millet improvement. But the recent availability of genomic data and advancement in omics tools has shown its enormous potential to enhance the efficiency and precision faced by conventional breeding in millet improvement. The development of high throughput genotyping platforms based on next-generation sequencing (NGS) has provided a low-cost method for genomic information, specifically for neglected nutri-rich cereals with the availability of a limited number of reference genome sequences. NGS has created new avenues for millet biotechnological interventions such as mutation-based study, GWAS, GS, and other omics technologies. The simultaneous discovery of high-throughput markers and multiplexed genotyping platform has aggressively aided marker-assisted breeding for millet improvement. Therefore, omics technology offers excellent opportunities to explore and combine useful variations for targeted traits that could impart high nutritional value to high-yielding cultivars under changing climatic conditions. In millet improvement, an in-depth account of NGS, integrating genomics data with different biotechnology tools, is reviewed in this context.
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Affiliation(s)
- Saurabh Pandey
- Department of Agricultural, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Ashutosh Singh
- Centre for Advanced Studies on Climate Change, RPCAU, Pusa, Samastipur, Bihar, 848125, India.
| | - Priyanka Jaiswal
- Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Mithilesh Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
| | - Khem Raj Meena
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Kishangarh, Rajasthan, 305817, India
| | - Satish Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
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Dwivedi SL, Chapman MA, Abberton MT, Akpojotor UL, Ortiz R. Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses. Front Genet 2023; 14:1193780. [PMID: 37396035 PMCID: PMC10311922 DOI: 10.3389/fgene.2023.1193780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.
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Affiliation(s)
| | - Mark A. Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Lv J, Xu Y, Dan X, Yang Y, Mao C, Ma X, Zhu J, Sun M, Jin Y, Huang L. Genomic survey of MYB gene family in six pearl millet (Pennisetum glaucum) varieties and their response to abiotic stresses. Genetica 2023:10.1007/s10709-023-00188-8. [PMID: 37266766 DOI: 10.1007/s10709-023-00188-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023]
Abstract
In addition to their roles in developmental and metabolic processes, MYB transcription factors play crucial roles in plant defense mechanisms and stress responses. A comprehensive analysis of six pearl millet genomes revealed the presence of 1133 MYB genes, which can be classified into four phylogenetically distinct subgroups. The duplication pattern of MYB genes across the pearl millet genomes demonstrates their conserved and similar evolutionary history. Overall, MYB genes were observed to be involved in drought and heat stress responses, with stronger differential expressed observed in root tissues. Multiple analyses indicated that MYB genes mediate abiotic stress responses by modulating abscisic acid-related pathways, circadian rhythms, and histone modification processes. A substantial number of duplicated genes were determined to exhibit differential expression under abiotic stress. The consistent positive expression trend observed in duplicated gene pairs, such as PMA5G04432.1 and PMA2G00728.1, across various abiotic stresses suggests that duplicated MYB genes plays a key role in the evolution of adaptive responses of pearl millet to abiotic stresses.
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Affiliation(s)
- Jinhang Lv
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Yue Xu
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Xuming Dan
- Department of The College of Life Sciences, Sichuan University, Sichuan, China
| | - Yuchen Yang
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Chunli Mao
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Xixi Ma
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Jie Zhu
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Min Sun
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Yarong Jin
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China
| | - Linkai Huang
- Department of Grassland Science and Technology, Sichuan Agricultural University, Sichuan, China.
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Huang B, Yan H, Sun M, Jin Y. Novel discovery in roles of structural variations and RWP-RK transcription factors in heat tolerance for pearl millet. STRESS BIOLOGY 2023; 3:12. [PMID: 37676357 PMCID: PMC10442032 DOI: 10.1007/s44154-023-00092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/03/2023] [Indexed: 09/08/2023]
Abstract
Global warming adversely affects crop production worldwide. Massive efforts have been undertaken to study mechanisms regulating heat tolerance in plants. However, the roles of structural variations (SVs) in heat stress tolerance remain unclear. In a recent article, Yan et al. (Nat Genet 1-12, 2023) constructed the first pan-genome of pearl millet (Pennisetum glaucum) and identified key SVs linked to genes involved in regulating plant tolerance to heat stress for an important crop with a superior ability to thrive in extremely hot and arid climates. Through multi-omics analyses integrating by pan-genomics, comparative genomics, transcriptomics, population genetics and and molecular biological technologies, they found RWP-RK transcription factors cooperating with endoplasmic reticulum-related genes play key roles in heat tolerance in pearl millet. The results in this paper provided novel insights to advance the understanding of the genetic and genomic basis of heat tolerance and an exceptional resource for molecular breeding to improve heat tolerance in pearl millet and other crops.
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Affiliation(s)
- Bingru Huang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA.
| | - Haidong Yan
- Department of Genetics, University of Georgia, Athens, GA, USA
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yarong Jin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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Shinde H, Dudhate A, Sathe A, Paserkar N, Wagh SG, Kadam US. Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet. PLANTS (BASEL, SWITZERLAND) 2023; 12:1412. [PMID: 36987099 PMCID: PMC10057621 DOI: 10.3390/plants12061412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/01/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Pearl millet is a significant crop that is tolerant to abiotic stresses and is a staple food of arid regions. However, its underlying mechanisms of stress tolerance are not fully understood. Plant survival is regulated by the ability to perceive a stress signal and induce appropriate physiological changes. Here, we screened for genes regulating physiological changes such as chlorophyll content (CC) and relative water content (RWC) in response to abiotic stress by using "weighted gene coexpression network analysis" (WGCNA) and clustering changes in physiological traits, i.e., CC and RWC associated with gene expression. Genes' correlations with traits were defined in the form of modules, and different color names were used to denote a particular module. Modules are groups of genes with similar patterns of expression, which also tend to be functionally related and co-regulated. In WGCNA, the dark green module (7082 genes) showed a significant positive correlation with CC, and the black (1393 genes) module was negatively correlated with CC and RWC. Analysis of the module positively correlated with CC highlighted ribosome synthesis and plant hormone signaling as the most significant pathways. Potassium transporter 8 and monothiol glutaredoxin were reported as the topmost hub genes in the dark green module. In Clust analysis, 2987 genes were found to display a correlation with increasing CC and RWC. Furthermore, the pathway analysis of these clusters identified the ribosome and thermogenesis as positive regulators of RWC and CC, respectively. Our study provides novel insights into the molecular mechanisms regulating CC and RWC in pearl millet.
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Affiliation(s)
- Harshraj Shinde
- Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA
| | - Ambika Dudhate
- Sequencing and Discovery Genomics Center, Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Atul Sathe
- Plant Science Department, McGill University, Macdonald Campus, Sainte Anne de Bellevue, QC H9X 3V9, Canada
| | - Neha Paserkar
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sopan Ganpatrao Wagh
- Department of Adaptive Biotechnology, Global Change Research Institute of the Czech Academy of Sciences, 60300 Brno, Czech Republic
| | - Ulhas Sopanrao Kadam
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Life Science (BK21 Four), Gyeongsang National University, Jinju-Daero, Jinju 52828, Gyeongnam-do, Republic of Korea
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Qu Y, Dudhate A, Shinde HS, Takano T, Tsugama D. Phylogenetic trees, conserved motifs and predicted subcellular localization for transcription factor families in pearl millet. BMC Res Notes 2023; 16:38. [PMID: 36941636 PMCID: PMC10029159 DOI: 10.1186/s13104-023-06305-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/06/2023] [Indexed: 03/22/2023] Open
Abstract
OBJECTIVES Pearl millet (Pennisetum glaucum) is a cereal crop that is tolerant to a high temperature, a drought and a nutrient-poor condition. Characterizing pearl millet proteins can help to improve productivity of pearl millet and other crops. Transcription factors in general are proteins that regulate transcription of their target genes and thereby regulate diverse processes. Some transcription factor families in pearl millet were characterized in previous studies, but most of them are not. The objective of the data presented was to characterize amino acid sequences for most transcription factors in pearl millet. DATA DESCRIPTION Sequences of 2395 pearl millet proteins that have transcription factor-associated domains were extracted. Subcellular and suborganellar localization of these proteins was predicted by MULocDeep. Conserved domains in these sequences were confirmed by CD-Search. These proteins were classified into 85 families on the basis of those conserved domains. A phylogenetic tree including pearl millet proteins and their counterparts in Arabidopsis thaliana and rice was constructed for each of these families. Sequence motifs were identified by MEME for each of these families.
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Affiliation(s)
- Yingwei Qu
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, 188-0002, Tokyo, Japan
| | - Ambika Dudhate
- Stowers Institute for Medical Research, 1000 East 50th Street, 64110, Kansas City, issouri, USA
| | | | - Tetsuo Takano
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, 188-0002, Tokyo, Japan
| | - Daisuke Tsugama
- Asian Research Center for Bioresource and Environmental Sciences (ARC-BRES), Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, 188-0002, Tokyo, Japan.
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Chaturvedi P, Govindaraj M, Sehgal D, Weckwerth W. Editorial: Sorghum and pearl millet as climate resilient crops for food and nutrition security, volume II. FRONTIERS IN PLANT SCIENCE 2023; 14:1170103. [PMID: 36968384 PMCID: PMC10031092 DOI: 10.3389/fpls.2023.1170103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Mahalingam Govindaraj
- HarvestPlus, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Deepmala Sehgal
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
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Kudapa H, Barmukh R, Vemuri H, Gorthy S, Pinnamaneni R, Vetriventhan M, Srivastava RK, Joshi P, Habyarimana E, Gupta SK, Govindaraj M. Genetic and genomic interventions in crop biofortification: Examples in millets. FRONTIERS IN PLANT SCIENCE 2023; 14:1123655. [PMID: 36950360 PMCID: PMC10025513 DOI: 10.3389/fpls.2023.1123655] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
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.
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Affiliation(s)
- Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Rutwik Barmukh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Hindu Vemuri
- International Maize and Wheat Improvement Center (CIMMYT), Patancheru, Telangana, India
| | - Sunita Gorthy
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | | | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Priyanka Joshi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - S. K. Gupta
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- HarvestPlus Program, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Kumar A, Sheoran P, Mann A, Yadav D, Kumar A, Devi S, Kumar N, Dhansu P, Sharma DK. Deciphering trait associated morpho-physiological responses in pearlmillet hybrids and inbred lines under salt stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1121805. [PMID: 36938010 PMCID: PMC10018183 DOI: 10.3389/fpls.2023.1121805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Pearl millet is a staple food for more than 90 million people residing in highly vulnerable hot arid and semi-arid regions of Africa and Asia. These regions are more prone to detrimental effects of soil salinity on crop performance in terms of reduced biomass and crop yields. We investigated the physiological mechanisms of salt tolerance to irrigation induced salinity stress (ECiw ~3, 6 & 9 dSm-1) and their confounding effects on plant growth and yield in pearl millet inbred lines and hybrids. On average, nearly 30% reduction in above ground plant biomass was observed at ECiw ~6 dSm-1 which stretched to 56% at ECiw ~9 dSm-1 in comparison to best available water. With increasing salinity stress, the crop performance of test hybrids was better in comparison to inbred lines; exhibiting relatively higher stomatal conductance (gS; 16%), accumulated lower proline (Pro; -12%) and shoot Na+/K+(-31%), synthesized more protein (SP; 2%) and sugars (TSS; 32%) compensating in lower biomass (AGB; -22%) and grain yield (GY: -14%) reductions at highest salinity stress of ECiw ~9 dSm-1. Physiological traits modeling underpinning plant salt tolerance and adaptation mechanism illustrated the key role of 7 traits (AGB, Pro, SS, gS, SPAD, Pn, and SP) in hybrids and 8 traits (AGB, Pro, PH, Na+, K+, Na+/K+, SPAD, and gS) in inbred lines towards anticipated grain yield variations in salinity stressed pearl millet. Most importantly, the AGB alone, explained >91% of yield variation among evaluated hybrids and inbreed lines at ECiw ~9 dSm-1. Cumulatively, the better morpho-physiological adaptation and lesser yield reduction with increasing salinity stress in pearl millet hybrids (HHB 146, HHB 272, and HHB 234) and inbred lines (H77/833-2-202, ICMA 94555 and ICMA 843-22) substantially complemented in increased plant salt tolerance and yield stability over a broad range of salinity stress. The information generated herein will help address in deciphering the trait associated physiological alterations to irrigation induced salt stress, and developing potential hybrids in pearl millet using these parents with special characteristics.
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Affiliation(s)
- Ashwani Kumar
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Parvender Sheoran
- Division of Social Sciences Research, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Anita Mann
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Devvart Yadav
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Arvind Kumar
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Sunita Devi
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Naresh Kumar
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
- Department of Chemistry and Biochemistry Eternal University, Baru, Sahib, India
| | - Pooja Dhansu
- ICAR–Sugarcane Breeding Institute, Regional Center, Karnal, India
| | - Dinesh K. Sharma
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, India
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Choudhary P, Shukla P, Muthamilarasan M. Genetic enhancement of climate-resilient traits in small millets: A review. Heliyon 2023; 9:e14502. [PMID: 37064482 PMCID: PMC10102230 DOI: 10.1016/j.heliyon.2023.e14502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/28/2023] Open
Abstract
Agriculture is facing the challenge of feeding the ever-growing population that is projected to reach ten billion by 2050. While improving crop yield and productivity can address this challenge, the increasing effects of global warming and climate change seriously threaten agricultural productivity. Thus, genomics and genome modification technologies are crucial to improving climate-resilient traits to enable sustained yield and productivity; however, significant research focuses on staple crops such as rice, wheat, and maize. Crops that are naturally climate-resilient and nutritionally superior to staple cereals, such as small millets, remain neglected and underutilized by mainstream research. The ability of small millets to grow in marginal regions having limited irrigation and poor soil fertility makes these crops a better choice for cultivation in arid and semi-arid areas. Hence, mainstreaming small millets for cultivation and using omics technologies to dissect the climate-resilient traits to identify the molecular determinants underlying these traits are imperative for addressing food and nutritional security. In this context, the review discusses the genomics and genome modification approaches for dissecting key traits in small millets and their application for improving these traits in cultivated germplasm. The review also discusses biofortification for nutritional security and machine-learning approaches for trait improvement in small millets. Altogether, the review provides a roadmap for the effective use of next-generation approaches for trait improvement in small millets. This will lead to the development of improved varieties for addressing multiple insecurities prevailing in the present climate change scenario.
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Yaadesh S, Tomar GS, Kaushik R, Prasanna R, Grover M. Azospirillum-Bacillus associations: synergistic effects on in vitro PGP traits and growth of pearl millet at early seedling stage under limited moisture conditions. 3 Biotech 2023; 13:90. [PMID: 36825258 PMCID: PMC9941397 DOI: 10.1007/s13205-023-03503-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/28/2023] [Indexed: 02/25/2023] Open
Abstract
The association of plant beneficial Azospirillum and Bacillus spp. strains expressing different sets of PGP traits may have complementary or supplementary effects on host plants. In the present investigation, A. formosense and Bacillus spp. strains showing diverse PGP traits (IAA production, nitrogenase activity, phosphate, zinc and potassium solubilization, siderophores, antagonism against phytopathogens, osmotic stress tolerance, etc.) were assessed for compatibility by cross-streaking and co-culturing. Under co-culture (Azospirillum + Bacillus), a significant increase in the expression of PGP traits, nitrogenase activity (up to 89%), phosphate solubilization (upto 236%), siderophore production (upto 20%) was observed as compared to individual Azospirillum culture, indicating synergistic effect of co-culture. IAA production was higher in Azospirillum sp. strains as compared to Bacillus spp. strains, when cultured individually; however, when co-cultured, the IAA levels were in the mid-range indicating the contributory effects of compatible strains. The effect of individual Azospirillum and Bacillus strains and their co-inoculation was also assessed on the growth of pearl millet at early stages under moisture-deficit stress imposed using PEG6000 (0, 10, and 20%). Co-inoculation enhanced seed germination (up to 10, 3, and 6% increase under 0, 10, and 20% PEG, respectively, over individual Azospirillum treatment), root traits (increased root hair density and lateral branches), and seedling vigor indices (up to 22, 32, 43% increase in seed vigor index I and 8, 14, and 10% increase in seed vigor index II under 0, 10, 20% PEG, respectively, over individual Azospirillum treatment) under normal as well as moisture-deficit conditions suggesting the role of Bacillus spp. strains in better adaptation of the plants to stress and higher yield potential. The synergistic effect of co-cultured Azospirillum and Bacillus strains on PGP traits indicated metabolic interplay between the two strains which needs to be further understood. The positive effect of co-inoculation on plant growth under moisture-deficit stress indicated the promise of Azospirillum and Bacillus as a synergistic bioformulation for combating nutrient and drought stress in pearl millet, particularly in nutrient-poor dryland agricultural systems. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03503-4.
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Affiliation(s)
- Sivakumar Yaadesh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Govind singh Tomar
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Minakshi Grover
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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Yan H, Sun M, Zhang Z, Jin Y, Zhang A, Lin C, Wu B, He M, Xu B, Wang J, Qin P, Mendieta JP, Nie G, Wang J, Jones CS, Feng G, Srivastava RK, Zhang X, Bombarely A, Luo D, Jin L, Peng Y, Wang X, Ji Y, Tian S, Huang L. Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nat Genet 2023; 55:507-518. [PMID: 36864101 PMCID: PMC10011142 DOI: 10.1038/s41588-023-01302-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/18/2023] [Indexed: 03/04/2023]
Abstract
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.
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Affiliation(s)
- Haidong Yan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | | | - Yarong Jin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ailing Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chuang Lin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bingchao Wu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Jing Wang
- Key Laboratory of Bio-Source and Environmental Conservation, School of Life Science, Sichuan University, Chengdu, China
| | - Peng Qin
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | | | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Chris S Jones
- Feed and Forage Development, International Livestock Research Institute, Nairobi, Kenya
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Aureliano Bombarely
- Instituto de Biologia Molecular y Celular de Plantas, UPV-CSIC, Valencia, Spain
| | - Dan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yang Ji
- Sichuan Animal Science Academy, Chengdu, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, China.
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
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Shrestha N, Hu H, Shrestha K, Doust AN. Pearl millet response to drought: A review. FRONTIERS IN PLANT SCIENCE 2023; 14:1059574. [PMID: 36844091 PMCID: PMC9955113 DOI: 10.3389/fpls.2023.1059574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
The C4 grass pearl millet is one of the most drought tolerant cereals and is primarily grown in marginal areas where annual rainfall is low and intermittent. It was domesticated in sub-Saharan Africa, and several studies have found that it uses a combination of morphological and physiological traits to successfully resist drought. This review explores the short term and long-term responses of pearl millet that enables it to either tolerate, avoid, escape, or recover from drought stress. The response to short term drought reveals fine tuning of osmotic adjustment, stomatal conductance, and ROS scavenging ability, along with ABA and ethylene transduction. Equally important are longer term developmental plasticity in tillering, root development, leaf adaptations and flowering time that can both help avoid the worst water stress and recover some of the yield losses via asynchronous tiller production. We examine genes related to drought resistance that were identified through individual transcriptomic studies and through our combined analysis of previous studies. From the combined analysis, we found 94 genes that were differentially expressed in both vegetative and reproductive stages under drought stress. Among them is a tight cluster of genes that are directly related to biotic and abiotic stress, as well as carbon metabolism, and hormonal pathways. We suggest that knowledge of gene expression patterns in tiller buds, inflorescences and rooting tips will be important for understanding the growth responses of pearl millet and the trade-offs at play in the response of this crop to drought. Much remains to be learnt about how pearl millet's unique combination of genetic and physiological mechanisms allow it to achieve such high drought tolerance, and the answers to be found may well be useful for crops other than just pearl millet.
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Affiliation(s)
- Nikee Shrestha
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, United States
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Hao Hu
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, United States
| | - Kumar Shrestha
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, United States
| | - Andrew N. Doust
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, United States
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