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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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2
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Khan A, Tian R, Bean SR, Yerka M, Jiao Y. Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in sorghum seeds. Commun Biol 2024; 7:841. [PMID: 38987396 PMCID: PMC11237005 DOI: 10.1038/s42003-024-06525-7] [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: 12/22/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Cereal seeds are vital for food, feed, and agricultural sustainability because they store and provide essential nutrients to human and animal food and feed systems. Unraveling molecular processes in seed development is crucial for enhancing cereal grain yield and quality. We analyze spatiotemporal transcriptome and metabolome profiles during sorghum seed development in the inbred line 'BTx623'. Morphological and molecular analyses identify the key stages of seed maturation, specifying starch biosynthesis onset at 5 days post-anthesis (dpa) and protein at 10 dpa. Transcriptome profiling from 1 to 25 dpa reveal dynamic gene expression pathways, shifting from cellular growth and embryo development (1-5 dpa) to cell division, fatty acid biosynthesis (5-25 dpa), and seed storage compounds synthesis in the endosperm (5-25 dpa). Network analysis identifies 361 and 207 hub genes linked to starch and protein synthesis in the endosperm, respectively, which will help breeders enhance sorghum grain quality. The availability of this data in the sorghum reference genome line establishes a baseline for future studies as new pangenomes emerge, which will consider copy number and presence-absence variation in functional food traits.
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Affiliation(s)
- Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Ran Tian
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Scott R Bean
- Grain Quality and Structure Research Unit, Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Melinda Yerka
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada-Reno, Reno, NV, 89557, USA
| | - Yinping Jiao
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
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Badiyal A, Mahajan R, Rana RS, Sood R, Walia A, Rana T, Manhas S, Jayswal DK. Synergizing biotechnology and natural farming: pioneering agricultural sustainability through innovative interventions. FRONTIERS IN PLANT SCIENCE 2024; 15:1280846. [PMID: 38584951 PMCID: PMC10995308 DOI: 10.3389/fpls.2024.1280846] [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: 08/21/2023] [Accepted: 01/29/2024] [Indexed: 04/09/2024]
Abstract
The world has undergone a remarkable transformation from the era of famines to an age of global food production that caters to an exponentially growing population. This transformation has been made possible by significant agricultural revolutions, marked by the intensification of agriculture through the infusion of mechanical, industrial, and economic inputs. However, this rapid advancement in agriculture has also brought about the proliferation of agricultural inputs such as pesticides, fertilizers, and irrigation, which have given rise to long-term environmental crises. Over the past two decades, we have witnessed a concerning plateau in crop production, the loss of arable land, and dramatic shifts in climatic conditions. These challenges have underscored the urgent need to protect our global commons, particularly the environment, through a participatory approach that involves countries worldwide, regardless of their developmental status. To achieve the goal of sustainability in agriculture, it is imperative to adopt multidisciplinary approaches that integrate fields such as biology, engineering, chemistry, economics, and community development. One noteworthy initiative in this regard is Zero Budget Natural Farming, which highlights the significance of leveraging the synergistic effects of both plant and animal products to enhance crop establishment, build soil fertility, and promote the proliferation of beneficial microorganisms. The ultimate aim is to create self-sustainable agro-ecosystems. This review advocates for the incorporation of biotechnological tools in natural farming to expedite the dynamism of such systems in an eco-friendly manner. By harnessing the power of biotechnology, we can increase the productivity of agro-ecology and generate abundant supplies of food, feed, fiber, and nutraceuticals to meet the needs of our ever-expanding global population.
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Affiliation(s)
- Anila Badiyal
- Department of Microbiology, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Rishi Mahajan
- Department of Microbiology, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Ranbir Singh Rana
- Centre for Geo-Informatics Research and Training, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Ruchi Sood
- Centre for Geo-Informatics Research and Training, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Abhishek Walia
- Department of Microbiology, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Tanuja Rana
- Department of Agricultural Biotechnology, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, Himachal Pradesh, India
| | - Shilpa Manhas
- Lovely Professional University, Phagwara, Punjab, India
| | - D. K. Jayswal
- National Agricultural Higher Education Project, Indian Council of Agricultural Research, New Delhi, India
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4
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Zhang H, Dean L, Wang ML, Dang P, Lamb M, Chen C. GWAS with principal component analysis identify QTLs associated with main peanut flavor-related traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1204415. [PMID: 37780495 PMCID: PMC10540862 DOI: 10.3389/fpls.2023.1204415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023]
Abstract
Peanut flavor is a complex and important trait affected by raw material and processing technology owing to its significant impact on consumer preference. In this research, principal component analysis (PCA) on 33 representative traits associated with flavor revealed that total sugars, sucrose, and total tocopherols provided more information related to peanut flavor. Genome-wide association studies (GWAS) using 102 U.S. peanut mini-core accessions were performed to study associations between 12,526 single nucleotide polymorphic (SNP) markers and the three traits. A total of 7 and 22 significant quantitative trait loci (QTLs) were identified to be significantly associated with total sugars and sucrose, respectively. Among these QTLs, four and eight candidate genes for the two traits were mined. In addition, two and five stable QTLs were identified for total sugars and sucrose in both years separately. No significant QTLs were detected for total tocopherols. The results from this research provide useful knowledge about the genetic control of peanut flavor, which will aid in clarifying the molecular mechanisms of flavor research in peanuts.
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Affiliation(s)
- Hui Zhang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Lisa Dean
- USDA-ARS Food Science and Market Quality and Handling Research Unit, Raleigh, NC, United States
| | - Ming Li Wang
- US Department of Agriculture-Agricultural Research Service Plant Genetic Resources Conservation, Griffin, GA, United States
| | - Phat Dang
- US Department of Agriculture-Agricultural Research Service National Peanut Research Laboratory, Dawson, GA, United States
| | - Marshall Lamb
- US Department of Agriculture-Agricultural Research Service National Peanut Research Laboratory, Dawson, GA, United States
| | - Charles Chen
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, United States
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5
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Kamal NM, Gorafi YSA, Tomemori H, Kim JS, Elhadi GMI, Tsujimoto H. Genetic variation for grain nutritional profile and yield potential in sorghum and the possibility of selection for drought tolerance under irrigated conditions. BMC Genomics 2023; 24:515. [PMID: 37660014 PMCID: PMC10474746 DOI: 10.1186/s12864-023-09613-w] [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: 03/28/2023] [Accepted: 08/22/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND Increasing grain nutritional value in sorghum (Sorghum bicolor) is a paramount breeding objective, as is increasing drought resistance (DR), because sorghum is grown mainly in drought-prone areas. The genetic basis of grain nutritional traits remains largely unknown. Marker-assisted selection using significant loci identified through genome-wide association study (GWAS) shows potential for selecting desirable traits in crops. This study assessed natural variation available in sorghum accessions from around the globe to identify novel genes or genomic regions with potential for improving grain nutritional value, and to study associations between DR traits and grain weight and nutritional composition. RESULTS We dissected the genetic architecture of grain nutritional composition, protein content, thousand-kernel weight (TKW), and plant height (PH) in sorghum through GWAS of 163 unique African and Asian accessions under irrigated and post-flowering drought conditions. Several QTLs were detected. Some were significantly associated with DR, TKW, PH, protein, and Zn, Mn, and Ca contents. Genomic regions on chromosomes 1, 2, 4, 8, 9, and 10 were associated with TKW, nutritional, and DR traits; colocalization patterns of these markers indicate potential for simultaneous improvement of these traits. In African accessions, markers associated with TKW were mapped to six regions also associated with protein, Zn, Ca, Mn, Na, and DR, suggesting the potential for simultaneous selection for higher grain nutrition and TKW. Our results indicate that it may be possible to select for increased DR on the basis of grain nutrition and weight potential. CONCLUSIONS This study provides a valuable resource for selecting landraces for use in plant breeding programs and for identifying loci that may contribute to grain nutrition and weight with the hope of producing cultivars that combine improved yield traits, nutrition, and DR.
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Affiliation(s)
- Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
- Agricultural Research Corporation, PO Box 126, Wad Medani, Sudan.
| | - Yasir Serag Alnor Gorafi
- Agricultural Research Corporation, PO Box 126, Wad Medani, Sudan
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
| | - Hisashi Tomemori
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - June-Sik Kim
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | | | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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6
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Pandey J, Thompson D, Joshi M, Scheuring DC, Koym JW, Joshi V, Vales MI. Genetic architecture of tuber-bound free amino acids in potato and effect of growing environment on the amino acid content. Sci Rep 2023; 13:13940. [PMID: 37626106 PMCID: PMC10457394 DOI: 10.1038/s41598-023-40880-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Free amino acids in potato tubers contribute to their nutritional value and processing quality. Exploring the natural variation in their accumulation in tubers across diverse genetic backgrounds is critical to potato breeding programs aiming to enhance or partition their distribution effectively. This study assessed variation in the tuber-bound free amino acids in a diversity panel of tetraploid potato clones developed and maintained by the Texas A&M Potato Breeding Program to explore their genetic basis and to obtain genomic-estimated breeding values for applied breeding purposes. Free amino acids content was evaluated in tubers of 217 tetraploid potato clones collected from Dalhart, Texas in 2019 and 2020, and Springlake, Texas in 2020. Most tuber amino acids were not affected by growing location, except histidine and proline, which were significantly lower (- 59.0%) and higher (+ 129.0%), respectively, at Springlake, Texas (a location that regularly suffers from abiotic stresses, mainly high-temperature stress). Single nucleotide polymorphism markers were used for genome-wide association studies and genomic selection of clones based on amino acid content. Most amino acids showed significant variations among potato clones and moderate to high heritabilities. Principal component analysis separated fresh from processing potato market classes based on amino acids distribution patterns. Genome-wide association studies discovered 33 QTL associated with 13 free amino acids. Genomic-estimated breeding values were calculated and are recommended for practical potato breeding applications to select parents and advance clones with the desired free amino acid content.
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Affiliation(s)
- Jeewan Pandey
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Dalton Thompson
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX, 78801, USA
| | - Madhumita Joshi
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX, 78801, USA
| | - Douglas C Scheuring
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Jeffrey W Koym
- Texas A&M AgriLife Research and Extension Center, Lubbock, TX, 79403, USA
| | - Vijay Joshi
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA.
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX, 78801, USA.
| | - M Isabel Vales
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA.
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Reta C, Asmellash T, Atlabachew M, Mehari B. Multielement analysis coupled with chemometrics modelling for geographical origin classification of teff [Eragrostis tef (Zuccagni) Trotter] grains from Amhara Region, Ethiopia. BMC Chem 2023; 17:50. [PMID: 37291660 DOI: 10.1186/s13065-023-00972-9] [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: 10/16/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Teff [Eragrostis tef (Zuccagni) Trotter] is an indigenous crop in Ethiopia, and Amhara region is the predominant teff producing region in the country. This study was aimed at developing an analytical methodology useful to determine the geographical origin of teff produced in the Amhara Region, based on multielement analysis combined with multivariate statistical techniques. For this, a total of 72 teff grain samples were collected from three zones (West Gojjam, East Gojjam, and Awi) and analysed for K, Na, Mg, Ca, Mn, Cu, Fe, Co, Ni, Zn, Cr, and Cd contents using inductively coupled plasma-optical emission spectroscopy (ICP-OES). The digestion and ICP-OES analysis method were accurate, with percentage recovery ranging 85.5 to 109% across the different metals analysed. Principal component analysis (PCA) and linear discriminant analysis (LDA) were applied to discriminate samples based on their production regions. Magnesium, Ca, Fe, Mn, and Zn were the most discriminating elements among the samples. The LDA model provided 96% correct classification of samples into production regions and varietal types, with an average prediction ability of 92%. Hence, the multielement analysis combined with statistical modeling can be used in the authentication of the geographical origin and varietal type of teff from Amhara region.
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Affiliation(s)
- Chaltu Reta
- Department of Chemistry, College of Science, Bahir Dar University, P.O.Box 79, Bahir Dar, Ethiopia
| | - Tihitinna Asmellash
- Department of Chemistry, College of Science, Bahir Dar University, P.O.Box 79, Bahir Dar, Ethiopia
| | - Minaleshewa Atlabachew
- Department of Chemistry, College of Science, Bahir Dar University, P.O.Box 79, Bahir Dar, Ethiopia.
| | - Bewketu Mehari
- Department of Chemistry, College of Natural and Computational Sciences, University of Gondar, P.O.Box 196, Gondar, Ethiopia.
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Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [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: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
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Zhang Y, Fan X, Liang D, Guo Q, Zhang X, Nie M, Li C, Meng S, Zhang X, Xu P, Guo W, Wang H, Liu Q, Wu Y. The Identification of a Yield-Related Gene Controlling Multiple Traits Using GWAS in Sorghum ( Sorghum bicolor L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1557. [PMID: 37050183 PMCID: PMC10097259 DOI: 10.3390/plants12071557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Sorghum bicolor (L.) is one of the oldest crops cultivated by human beings which has been used in food and wine making. To understand the genetic diversity of sorghum breeding resources and further guide molecular-marker-assisted breeding, six yield-related traits were analyzed for 214 sorghum germplasm from all over the world, and 2,811,016 single-nucleotide polymorphisms (SNPs) markers were produced by resequencing these germplasms. After controlling Q and K, QTLs were found to be related to the traits using three algorisms. Interestingly, an important QTL was found which may affect multiple traits in this study. It was the most likely candidate gene for the gene SORBI_3008G116500, which was a homolog of Arabidopsis thaliana gene-VIP5 found by analyzing the annotation of the gene in the LD block. The haplotype analysis showed that the SORBI_3008G116500hap3 was the elite haplotype, and it only existed in Chinese germplasms. The traits were proven to be more associated with the SNPs of the SORBI_3008G116500 promoter through gene association studies. Overall, the QTLs and the genes identified in this study would benefit molecular-assisted yield breeding in sorghum.
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Affiliation(s)
- Yizhong Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Xinqi Fan
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Du Liang
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Qi Guo
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Xiaojuan Zhang
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Mengen Nie
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Chunhong Li
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Shan Meng
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xianggui Zhang
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Peng Xu
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Wenqi Guo
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Huiyan Wang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Qingshan Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Yuxiang Wu
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
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10
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Boatwright JL, Sapkota S, Kresovich S. Functional genomic effects of indels using Bayesian genome-phenome wide association studies in sorghum. Front Genet 2023; 14:1143395. [PMID: 37065477 PMCID: PMC10102435 DOI: 10.3389/fgene.2023.1143395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
High-throughput genomic and phenomic data have enhanced the ability to detect genotype-to-phenotype associations that can resolve broad pleiotropic effects of mutations on plant phenotypes. As the scale of genotyping and phenotyping has advanced, rigorous methodologies have been developed to accommodate larger datasets and maintain statistical precision. However, determining the functional effects of associated genes/loci is expensive and limited due to the complexity associated with cloning and subsequent characterization. Here, we utilized phenomic imputation of a multi-year, multi-environment dataset using PHENIX which imputes missing data using kinship and correlated traits, and we screened insertions and deletions (InDels) from the recently whole-genome sequenced Sorghum Association Panel for putative loss-of-function effects. Candidate loci from genome-wide association results were screened for potential loss of function using a Bayesian Genome-Phenome Wide Association Study (BGPWAS) model across both functionally characterized and uncharacterized loci. Our approach is designed to facilitate in silico validation of associations beyond traditional candidate gene and literature-search approaches and to facilitate the identification of putative variants for functional analysis and reduce the incidence of false-positive candidates in current functional validation methods. Using this Bayesian GPWAS model, we identified associations for previously characterized genes with known loss-of-function alleles, specific genes falling within known quantitative trait loci, and genes without any previous genome-wide associations while additionally detecting putative pleiotropic effects. In particular, we were able to identify the major tannin haplotypes at the Tan1 locus and effects of InDels on the protein folding. Depending on the haplotype present, heterodimer formation with Tan2 was significantly affected. We also identified major effect InDels in Dw2 and Ma1, where proteins were truncated due to frameshift mutations that resulted in early stop codons. These truncated proteins also lost most of their functional domains, suggesting that these indels likely result in loss of function. Here, we show that the Bayesian GPWAS model is able to identify loss-of-function alleles that can have significant effects upon protein structure and folding as well as multimer formation. Our approach to characterize loss-of-function mutations and their functional repercussions will facilitate precision genomics and breeding by identifying key targets for gene editing and trait integration.
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Affiliation(s)
- J. Lucas Boatwright
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- *Correspondence: J. Lucas Boatwright,
| | - Sirjan Sapkota
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - Stephen Kresovich
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Feed the Future Innovation Lab for Crop Improvement, Cornell University, Ithaca, NY, United States
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La Borde N, Rajewski J, Dweikat I. Novel QTL for chilling tolerance at germination and early seedling stages in sorghum. Front Genet 2023; 14:1129460. [PMID: 37007950 PMCID: PMC10052408 DOI: 10.3389/fgene.2023.1129460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
Sorghum (Sorghum bicolor L.) a drought tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importanceorghum’s originated from tropical regions rendering the crop to be cold sensitive. Low temperature stresses such as chilling and frost greatly affect the agronomic performance of sorghum and limit its geographical distribution, posing a major problem in temperate environments when sorghum is planted early. Understanding the genetic basis of wide adaptability and of sorghum would facilitate molecular breeding programs and studies of other C4 crops. The objective of this study is to conduct quantitative trait loci analysis using genotying by sequencing for early seed germination and seedling cold tolerance in two sorghum recombinant inbred lines populations. To accomplish that, we used two populations of recombinant inbred lines (RIL) developed from crosses between cold-tolerant (CT19, ICSV700) and cold-sensitive (TX430, M81E) parents. The derived RIL populations were evaluated for single nucleotide polymorphism (SNP) using genotype-by-sequencing (GBS) in the field and under controlled environments for their response to chilling stress. Linkage maps were constructed with 464 and 875 SNPs for the CT19 X TX430 (C1) and ICSV700 X M81 E (C2) populations respectively. Using quantitative trait loci (QTL) mapping, we identified QTL conferring tolerance to chilling tolerance at the seedling stage. A total of 16 and 39 total QTL were identified in the C1 and C2 populations, respectively. Two major QTL were identified in the C1 population, and three major QTL were mapped in the C2 population. Comparisons between the two populations and with previously identified QTL show a high degree of similarity in QTL locations. Given the amount of co-localization of QTL across traits and the direction of allelic effect supports that these regions have a pleiotropic effect. These QTL regions were also identified to be highly enriched for genes encoding chilling stress and hormonal response genes. This identified QTL can be useful in developing tools for molecular breeding of sorghums with improved low-temperature germinability.
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Wenndt A, Boyles R, Ackerman A, Sapkota S, Repka A, Nelson R. Host Determinants of Fungal Species Composition and Symptom Manifestation in the Sorghum Grain Mold Disease Complex. PLANT DISEASE 2023; 107:315-325. [PMID: 36800304 DOI: 10.1094/pdis-03-22-0675-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Sorghum grain mold (SGM) is an important multifungal disease complex affecting sorghum (Sorghum bicolor) production systems worldwide. SGM-affected sorghum grain can be contaminated with potent fumonisin mycotoxins produced by Fusarium verticillioides, a prevalent SGM-associated taxon. Historically, efforts to improve resistance to SGM have achieved only limited success. Classical approaches to evaluating SGM resistance are based solely on disease severity, which offers little insight regarding the distinct symptom manifestations within the disease complex. In this study, three novel phenotypes were developed to facilitate assessment of SGM symptom manifestation. A sorghum diversity panel composed of 390 accessions was inoculated with endogenous strains of F. verticillioides and evaluated for these phenotypes, as well as for the conventional panicle grain mold severity rating phenotype, in South Carolina, U.S.A., in 2017 and 2019. Distributions of phenotype values were examined, broad-sense heritability was estimated, and relationships to botanical race were explored. A typology of SGM symptom manifestations was developed to classify accessions using principal component analysis and k-means clustering, constituting a novel option for basing breeding decisions on SGM outcomes more nuanced than disease severity. Genome-wide association studies were performed using SGM trait data, resulting in the identification of 19 significant single nucleotide polymorphisms in linkage disequilibrium with a total of 86 gene models. Our findings provide a basis of exploratory evidence regarding the genetic architecture of SGM symptom manifestation and indicate that traits other than disease severity could be tractable targets for SGM resistance breeding.
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Affiliation(s)
- Anthony Wenndt
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Richard Boyles
- Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC 29506
| | - Arlyn Ackerman
- Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC 29506
| | - Sirjan Sapkota
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634
| | - Ace Repka
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Rebecca Nelson
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
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Berdugo-Cely JA, Céron-Lasso MDS, Yockteng R. Phenotypic and molecular analyses in diploid and tetraploid genotypes of Solanum tuberosum L. reveal promising genotypes and candidate genes associated with phenolic compounds, ascorbic acid contents, and antioxidant activity. FRONTIERS IN PLANT SCIENCE 2023; 13:1007104. [PMID: 36743552 PMCID: PMC9889998 DOI: 10.3389/fpls.2022.1007104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/08/2022] [Indexed: 06/18/2023]
Abstract
Potato tubers contain biochemical compounds with antioxidant properties that benefit human health. However, the genomic basis of the production of antioxidant compounds in potatoes has largely remained unexplored. Therefore, we report the first genome-wide association study (GWAS) based on 4488 single nucleotide polymorphism (SNP) markers and the phenotypic evaluation of Total Phenols Content (TPC), Ascorbic Acid Content (AAC), and Antioxidant Activity (AA) traits in 404 diverse potato genotypes (84 diploids and 320 tetraploids) conserved at the Colombian germplasm bank that administers AGROSAVIA. The concentration of antioxidant compounds correlated to the skin tuber color and ploidy level. Especially, purple-blackish tetraploid tubers had the highest TPC (2062.41 ± 547.37 mg GAE), while diploid pink-red tubers presented the highest AA (DDPH: 14967.1 ± 4687.79 μmol TE; FRAP: 2208.63 ± 797.35 mg AAE) and AAC (4.52 mg ± 0.68 AA). The index selection allowed us to choose 20 promising genotypes with the highest values for the antioxidant compounds. Genome Association mapping identified 58 SNP-Trait Associations (STAs) with single-locus models and 28 Quantitative Trait Nucleotide (QTNs) with multi-locus models associated with the evaluated traits. Among models, eight STAs/QTNs related to TPC, AAC, and AA were detected in common, flanking seven candidate genes, from which four were pleiotropic. The combination in one population of diploid and tetraploid genotypes enabled the identification of more genetic associations. However, the GWAS analysis implemented independently in populations detected some regions in common between diploids and tetraploids not detected in the mixed population. Candidate genes have molecular functions involved in phenolic compounds, ascorbic acid biosynthesis, and antioxidant responses concerning plant abiotic stress. All candidate genes identified in this study can be used for further expression analysis validation and future implementation in marker-assisted selection pre-breeding platforms targeting fortified materials. Our study further revealed the importance of potato germplasm conserved in national genebanks, such as AGROSAVIA's, as a valuable genetic resource to improve existing potato varieties.
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Affiliation(s)
- Jhon A. Berdugo-Cely
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Turipaná, Km 13 vía Montería-Cereté, Montería, Córdoba, Colombia
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
| | - María del Socorro Céron-Lasso
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
| | - Roxana Yockteng
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, National Museum of Natural History, Paris, France
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Diatta-Holgate E, Hugghis E, Weil C, Faye JM, Danquah A, Diatta C, Tongoona P, Danquah EY, Cisse N, Tuinstra MR. Natural variability for protein digestibility and grain quality traits in a West African Sorghum Association Panel. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Paiva CL, Netto DA, Queiroz VA, Gloria MBA. Germinated sorghum (Sorghum bicolor L.) and seedlings show expressive contents of putrescine. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Hao H, Li Z, Leng C, Lu C, Luo H, Liu Y, Wu X, Liu Z, Shang L, Jing HC. Sorghum breeding in the genomic era: opportunities and challenges. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1899-1924. [PMID: 33655424 PMCID: PMC7924314 DOI: 10.1007/s00122-021-03789-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/05/2021] [Indexed: 05/04/2023]
Abstract
The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities.
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Affiliation(s)
- Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhigang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chuanyuan Leng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Cheng Lu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiquan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- Engineering Laboratory for Grass-based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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17
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Berhe M, Dossa K, You J, Mboup PA, Diallo IN, Diouf D, Zhang X, Wang L. Genome-wide association study and its applications in the non-model crop Sesamum indicum. BMC PLANT BIOLOGY 2021; 21:283. [PMID: 34157965 PMCID: PMC8218510 DOI: 10.1186/s12870-021-03046-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/17/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Sesame is a rare example of non-model and minor crop for which numerous genetic loci and candidate genes underlying features of interest have been disclosed at relatively high resolution. These progresses have been achieved thanks to the applications of the genome-wide association study (GWAS) approach. GWAS has benefited from the availability of high-quality genomes, re-sequencing data from thousands of genotypes, extensive transcriptome sequencing, development of haplotype map and web-based functional databases in sesame. RESULTS In this paper, we reviewed the GWAS methods, the underlying statistical models and the applications for genetic discovery of important traits in sesame. A novel online database SiGeDiD ( http://sigedid.ucad.sn/ ) has been developed to provide access to all genetic and genomic discoveries through GWAS in sesame. We also tested for the first time, applications of various new GWAS multi-locus models in sesame. CONCLUSIONS Collectively, this work portrays steps and provides guidelines for efficient GWAS implementation in sesame, a non-model crop.
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Affiliation(s)
- Muez Berhe
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
- Humera Agricultural Research Center of Tigray Agricultural Research Institute, Humera, Tigray, Ethiopia
| | - Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China.
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal.
- Laboratory of Genetics, Horticulture and Seed Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526, Cotonou, Republic of Benin.
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Pape Adama Mboup
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Idrissa Navel Diallo
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China.
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Chadalavada K, Kumari BDR, Kumar TS. Sorghum mitigates climate variability and change on crop yield and quality. PLANTA 2021; 253:113. [PMID: 33928417 DOI: 10.1007/s00425-021-03631-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/17/2021] [Indexed: 06/12/2023]
Abstract
Global food insecurity concerns due to climate change, emphasizes the need to focus on the sensitivity of sorghum to climate change and potential crop improvement strategies available, which is discussed in the current review to promote climate-smart agriculture. Climate change effects immensely disturb the global agricultural systems by reducing crop production. Changes in extreme weather and climate events such as high-temperature episodes and extreme rainfalls events, droughts, flooding adversely affect the production of staple food crops, posing threat to ecosystem resilience. The resulting crop losses lead to food insecurity and poverty and question the sustainable livelihoods of small farmer communities, particularly in developing countries. In view of this, it is essential to focus and adapt climate-resilient food crops which need lower inputs and produce sustainable yields through various biotic and abiotic stress-tolerant traits. Sorghum, "the camel of cereals", is one such climate-resilient food crop that is less sensitive to climate change vulnerabilities and also an important staple food in many parts of Asia and Africa. It is a rainfed crop and provides many essential nutrients. Understanding sorghum's sensitivity to climate change provides scope for improvement of the crop both in terms of quantity and quality and alleviates food and feed security in future climate change scenarios. Thus, the current review focused on understanding the sensitivity of sorghum crop to various stress events due to climate change and throws light on different crop improvement strategies available to pave the way for climate-smart agriculture.
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Affiliation(s)
- Keerthi Chadalavada
- Department of Botany, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India.
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India.
| | - B D Ranjitha Kumari
- Department of Botany, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - T Senthil Kumar
- Department of Botany, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
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Ruperao P, Thirunavukkarasu N, Gandham P, Selvanayagam S, Govindaraj M, Nebie B, Manyasa E, Gupta R, Das RR, Odeny DA, Gandhi H, Edwards D, Deshpande SP, Rathore A. Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain. FRONTIERS IN PLANT SCIENCE 2021; 12:666342. [PMID: 34140962 PMCID: PMC8204017 DOI: 10.3389/fpls.2021.666342] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/28/2021] [Indexed: 05/05/2023]
Abstract
Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.
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Affiliation(s)
- Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | | | - Prasad Gandham
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | | | | | - Baloua Nebie
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, Mali
| | - Eric Manyasa
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Roma Rani Das
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Damaris A. Odeny
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Harish Gandhi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Santosh P. Deshpande
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
- Santosh P. Deshpande
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
- *Correspondence: Abhishek Rathore
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Identification of potential QTLs and genes associated with seed composition traits in peanut (Arachis hypogaea L.) using GWAS and RNA-Seq analysis. Gene 2020; 769:145215. [PMID: 33038422 DOI: 10.1016/j.gene.2020.145215] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 11/21/2022]
Abstract
Cultivated peanut (Arachis hypogaea L.) is a major oilseed crop providing edible oil and protein. Oil quality is determined by fatty acid composition including the ratio of oleic acid (C18:1) and linoleic acid (C18:2). A genome-wide association study with 13,382 single nucleotide polymorphisms (SNPs) was conducted to investigate the genetics basis of oil, protein, eight fatty acid concentrations, and O/L ratio (ratio of oleic and linoleic acid) using a diverse panel of 120 genotypes mainly selected from the U.S. peanut mini core collection grown in two years. A total of 178 significant quantitative trait loci (QTLs) associated with those seed composition traits were identified with phenotypic variation explained (PVE) from 18.35% to 27.56%. RNA-Seq analysis identified 282 DEGs (differentially expressed genes) within the 1 Mb of the significant QTLs for seed composition traits. Among those 282 genes, sixteen candidate genes for seed fatty acid metabolism and protein synthesis were screened according to the gene functions.
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21
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Elango D, Xue W, Chopra S. Genome wide association mapping of epi-cuticular wax genes in Sorghum bicolor. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1727-1737. [PMID: 32801499 PMCID: PMC7415066 DOI: 10.1007/s12298-020-00848-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/11/2020] [Accepted: 07/07/2020] [Indexed: 05/25/2023]
Abstract
Sorghum accumulates epi-cuticular wax (EW) in leaves, sheaths, and culms. EW reduces the transpirational and nontranspirational (nonstomatal) water loss and protects the plant from severe drought stress in addition to imparting resistance against insect pests. Results presented here are from the analysis of EW content of 387 diverse sorghum accessions and its genome-wide association study (GWAS). EW content in sorghum leaves ranged from 0.1 to 29.7 mg cm-2 with a mean value of 5.1 mg cm-2. GWAS using 265,487 single nucleotide polymorphisms identified thirty-seven putative genes associated (P < 9.89E-06) with EW biosynthesis and transport in sorghum. Major EW biosynthetic genes identified included 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, an Ankyrin repeat protein, a bHLH-MYC, and an R2R3-MYB transcription factor. Genes involved in EW regulation or transport included an ABC transporter, a Lipid exporter ABCA1, a Multidrug resistance protein, Inositol 1, 3, 4-trisphosphate 5/6-kinase, and a Cytochrome P450. This GWA study thus demonstrates the potential for genetic manipulation of EW content in sorghum for better adaptation to biotic and abiotic stress.
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Affiliation(s)
- Dinakaran Elango
- Department of Plant Science, Penn State University, University Park, PA USA
| | - Weiya Xue
- Department of Plant Science, Penn State University, University Park, PA USA
| | - Surinder Chopra
- Department of Plant Science, Penn State University, University Park, PA USA
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