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Prakash NR, Kumar K, Muthusamy V, Zunjare RU, Hossain F. Unique genetic architecture of prolificacy in 'Sikkim Primitive' maize unraveled through whole-genome resequencing-based DNA polymorphism. PLANT CELL REPORTS 2024; 43:134. [PMID: 38702564 DOI: 10.1007/s00299-024-03176-0] [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: 10/16/2023] [Accepted: 02/13/2024] [Indexed: 05/06/2024]
Abstract
KEY MESSAGE 'Sikkim Primitive' maize landrace, unique for prolificacy (7-9 ears per plant) possesses unique genomic architecture in branching and inflorescence-related gene(s), and locus Zm00001eb365210 encoding glycosyltransferases was identified as the putative candidate gene underlying QTL (qProl-SP-8.05) for prolificacy. The genotype possesses immense usage in breeding high-yielding baby-corn genotypes. 'Sikkim Primitive' is a native landrace of North Eastern Himalayas, and is characterized by having 7-9 ears per plant compared to 1-2 ears in normal maize. Though 'Sikkim Primitive' was identified in the 1960s, it has not been characterized at a whole-genome scale. Here, we sequenced the entire genome of an inbred (MGUSP101) derived from 'Sikkim Primitive' along with three non-prolific (HKI1128, UMI1200, and HKI1105) and three prolific (CM150Q, CM151Q and HKI323) inbreds. A total of 942,417 SNPs, 24,160 insertions, and 27,600 deletions were identified in 'Sikkim Primitive'. The gene-specific functional mutations in 'Sikkim Primitive' were classified as 10,847 missense (54.36%), 402 non-sense (2.015%), and 8,705 silent (43.625%) mutations. The number of transitions and transversions specific to 'Sikkim Primitive' were 666,021 and 279,950, respectively. Among all base changes, (G to A) was the most frequent (215,772), while (C to G) was the rarest (22,520). Polygalacturonate 4-α-galacturonosyltransferase enzyme involved in pectin biosynthesis, cell-wall organization, nucleotide sugar, and amino-sugar metabolism was found to have unique alleles in 'Sikkim Primitive'. The analysis further revealed the Zm00001eb365210 gene encoding glycosyltransferases as the putative candidate underlying QTL (qProl-SP-8.05) for prolificacy in 'Sikkim Primitive'. High-impact nucleotide variations were found in ramosa3 (Zm00001eb327910) and zeaxanthin epoxidase1 (Zm00001eb081460) genes having a role in branching and inflorescence development in 'Sikkim Primitive'. The information generated unraveled the genetic architecture and identified key genes/alleles unique to the 'Sikkim Primitive' genome. This is the first report of whole-genome characterization of the 'Sikkim Primitive' landrace unique for its high prolificacy.
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Affiliation(s)
- Nitish Ranjan Prakash
- ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012, India
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, 132001, India
| | - Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, Delhi, 110012, India
| | - Vignesh Muthusamy
- ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012, India
| | | | - Firoz Hossain
- ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, 110012, India.
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Choudhary M, Singh A, Das MM, Kumar P, Naliath R, Singh V, Kumar B, Rakshit S. Morpho-physiological traits and SSR markers-based analysis of relationships and genetic diversity among fodder maize landraces in India. Mol Biol Rep 2023; 50:6829-6841. [PMID: 37392281 DOI: 10.1007/s11033-023-08602-2] [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: 03/22/2023] [Accepted: 06/15/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND Maize is an excellent fodder crop due to its high biomass, better palatability, succulency, and nutrition. Studies on morpho-physiological and biochemical characterization of fodder maize are limited. The present study aimed to explore the genetic variation in fodder maize landraces for various morpho-physiological traits and estimation of genetic relationship and population structure. METHODS AND RESULTS The study on 47 fodder maize landraces revealed significant variation for all morpho-physiological traits except leaf-stem ratio. Plant height, stem girth, leaf-width and number of leaves showed positive correlation with green fodder yield. Morpho-physiological traits-based clustering grouped the landraces into three major clusters, whereas neighbour joining cluster and population structure analysis using 40 SSR markers revealed four and five major groups, respectively. Most landraces of Northern Himalaya-Kashmir and Ludhiana fall into a single group, whereas rest groups mainly had landraces from North-Eastern Himalaya. A total of 101 alleles were generated with mean polymorphic information content value of 0.36 and major allele frequency of 0.68. The pair wise genetic dissimilarity between genotypes ranged from 0.21 to 0.67. Mantel test revealed weak but significant correlation between morphological and molecular distance. Biochemical characterisation of superior landraces revealed significant variation for neutral detergent fibre, acid detergent fibre, cellulose and lignin content. CONCLUSION Interestingly, significant, and positive correlation of SPAD with lignin content can be explored to bypass the costly affair of invitro quality assessment for digestibility parameters. The study identified superior landraces and demonstrated the use of molecular markers in genetic diversity assessment and grouping of genotypes for fodder maize improvement.
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Affiliation(s)
- Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
- School of Agriculture and Environment, Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Alla Singh
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
| | - M M Das
- ICAR-Indian Grassland and Forage Research Institute, Jhansi, 284003, Uttar Pradesh, India
| | - Pardeep Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India.
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, 84322, USA.
| | - Ritu Naliath
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
| | - Vishal Singh
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010, Jharkhand, India
| | - Bhupender Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001, Punjab, India
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010, Jharkhand, India
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Mathiang EA, Sa KJ, Park H, Kim YJ, Lee JK. Genetic Diversity and Population Structure of Normal Maize Germplasm Collected in South Sudan Revealed by SSR Markers. PLANTS (BASEL, SWITZERLAND) 2022; 11:2787. [PMID: 36297809 PMCID: PMC9611378 DOI: 10.3390/plants11202787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Maize is one of the leading global cereals, and in South Sudan maize cultivation occurs in nearly all of the country's agro-ecological zones. Despite its widespread cultivation, farmers in South Sudan depend on undeveloped varieties, which results in very low yields in the field. In the current study, 27 simple sequence repeat (SSR) markers were used to investigate genetic diversity and population structures among 37 landrace maize accessions collected from farmers' fields in South Sudan. In total, 200 alleles were revealed with an average of 7.4 alleles per locus and a range from 3.0 to 13.0 alleles per locus. The observed heterozygosity values ranged from 0.06 to 0.91 with an average of 0.35. High polymorphic information content (PIC) values were identified with a mean of 0.69, which indicates the informativeness of the chosen SSR loci. Genetic structure analysis revealed a moderate genetic differentiation among the maize populations with a fixation index of 0.16, while there was very high genetic differentiation within the groups of populations of three regions with a mean fixation index (F) of 0.37. An unweighted pair group method with an arithmetic mean (UPGMA) dendrogram clustered the 37 maize accessions into three groups with 43% genetic similarity. The clustering pattern of the maize accessions was moderately consistent with their collection area. The findings of this study will provide maize breeders with a better understanding of maize diversification as well as a reserve of genetic resources for use in the selection of advantageous and useful resources for the development of maize varieties in South Sudan.
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Affiliation(s)
- Emmanuel Andrea Mathiang
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Kyu Jin Sa
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Hyeon Park
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Korea
| | - Yeon Joon Kim
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Ju Kyong Lee
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, Korea
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Kumar B, Rakshit S, Kumar S, Singh BK, Lahkar C, Jha AK, Kumar K, Kumar P, Choudhary M, Singh SB, Amalraj JJ, Prakash B, Khulbe R, Kamboj MC, Chirravuri NN, Hossain F. Genetic Diversity, Population Structure and Linkage Disequilibrium Analyses in Tropical Maize Using Genotyping by Sequencing. PLANTS (BASEL, SWITZERLAND) 2022; 11:799. [PMID: 35336681 PMCID: PMC8955159 DOI: 10.3390/plants11060799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Several maize breeding programs in India have developed numerous inbred lines but the lines have not been characterized using high-density molecular markers. Here, we studied the molecular diversity, population structure, and linkage disequilibrium (LD) patterns in a panel of 314 tropical normal corn, two sweet corn, and six popcorn inbred lines developed by 17 research centers in India, and 62 normal corn from the International Maize and Wheat Improvement Center (CIMMYT). The 384 inbred lines were genotyped with 60,227 polymorphic single nucleotide polymorphisms (SNPs). Most of the pair-wise relative kinship coefficients (58.5%) were equal or close to 0, which suggests the lack of redundancy in the genomic composition in the majority of inbred lines. Genetic distance among most pairs of lines (98.3%) varied from 0.20 to 0.34 as compared with just 1.7% of the pairs of lines that differed by <0.20, which suggests greater genetic variation even among sister lines. The overall average of 17% heterogeneity was observed in the panel indicated the need for further inbreeding in the high heterogeneous genotypes. The mean nucleotide diversity and frequency of polymorphic sites observed in the panel were 0.28 and 0.02, respectively. The model-based population structure, principal component analysis, and phylogenetic analysis revealed three to six groups with no clear patterns of clustering by centers-wise breeding lines, types of corn, kernel characteristics, maturity, plant height, and ear placement. However, genotypes were grouped partially based on their source germplasm from where they derived.
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Affiliation(s)
- Bhupender Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Sonu Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Brijesh Kumar Singh
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Chayanika Lahkar
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Abhishek Kumar Jha
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Krishan Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Pardeep Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - Shyam Bir Singh
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India; (B.K.); (S.K.); (B.K.S.); (C.L.); (A.K.J.); (K.K.); (P.K.); (M.C.); (S.B.S.)
| | - John J. Amalraj
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India;
| | - Bhukya Prakash
- ICAR-Directorate of Poultry Research, Hyderabad 500030, India;
| | - Rajesh Khulbe
- Department of Crop Imrovement, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora 263601, India;
| | - Mehar Chand Kamboj
- Department of Plant Breeding, CCS-Haryana Agricultural University, Regional Research Station, Uchani 132001, India;
| | - Neeraja N. Chirravuri
- Department of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India;
| | - Firoz Hossain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
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Soliman ERS, El-Shazly HH, Börner A, Badr A. Genetic diversity of a global collection of maize genetic resources in relation to their subspecies assignments, geographic origin, and drought tolerance. BREEDING SCIENCE 2021; 71:313-325. [PMID: 34776738 PMCID: PMC8573557 DOI: 10.1270/jsbbs.20142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/21/2021] [Indexed: 06/13/2023]
Abstract
The genetic diversity among an international collection of 40 maize accessions has been evaluated using DNA ISSR fingerprinting. Among the 180 ISSR markers scored by 15 primers, 161 markers (89.59%) were polymorphic and 19 were unique in 16 accessions. A cluster tree based on the average distance coefficients and the Dice similarity indices divided the accessions into three major groups, each including clusters of accessions assigned to their subspecies. However, a low level of genetic differentiation among the accessions was demonstrated by the STRUCTURE analysis of ISSR data in agreement with the low gene flow (Nm) value among the accessions. A scatter diagram of the principal component analysis (PCA) based on ISSR data analysis revealed that the accessions were differentiated into three groups comparable to those produced by the cluster analysis, in which some accessions of the same subspecies showed a close similarity to each other. A scatter diagram of the principal coordinate analysis (PCoA) based on the drought tolerance indices (DTIs) showed that nine genetically similar accessions share drought tolerance characteristics; these include four of subsp. indurata, three of subsp. everata, and two of subsp. indentata. An abundance of unique ISSR alleles found in the 16 accessions, including the nine drought-tolerant accessions, represents rich untapped genetic resources and these accessions may be exploited in the future breeding of maize commercial lines.
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Affiliation(s)
- Elham R. S. Soliman
- Botany and Microbiology Department, Faculty of Science, Helwan University, Cairo 11421, Egypt
| | - Hanaa H. El-Shazly
- Biological and Geological Sciences Department, Faulty of Education, Ain Shams University, Cairo, Egypt
| | - Andreas Börner
- Gene Bank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Abdelfattah Badr
- Botany and Microbiology Department, Faculty of Science, Helwan University, Cairo 11421, Egypt
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Diaw Y, Tollon-Cordet C, Charcosset A, Nicolas SD, Madur D, Ronfort J, David J, Gouesnard B. Genetic diversity of maize landraces from the South-West of France. PLoS One 2021; 16:e0238334. [PMID: 33524023 PMCID: PMC7850504 DOI: 10.1371/journal.pone.0238334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/15/2021] [Indexed: 11/30/2022] Open
Abstract
From the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France (SWF), a traditional region for maize cultivation. A set of landraces were collected in this area between the 1950s and 1980s and were then conserved ex situ in a germplam collection. Previous studies using molecular markers on approx. twenty landraces from this region suggested that they belonged to a Pyrenees-Galicia Flint genetic group and originated from hybridizations between Caribbean and Northern Flint germplasms introduced to Europe. In this study, we assessed the structure and genetic diversity of 194 SWF maize landraces to better elucidate their origin, using a 50K SNP array and a bulk DNA approach. We identified two weakly differentiated genetic groups, one in the Western part and the other in the Eastern part of the studied region. We highlighted the existence of a longitudinal gradient along the SWF area that was probably maintained through the interplay between genetic drifts and restricted gene flows. The contact zone between the two groups observed near the Garonne valley may be the result of these evolutionnary forces. We found in landraces from the East part of the region significant cases of admixture between landraces from the Northern Flint group and landraces from either the Caribbean, Andean or Italian groups. We then assumed that SWF landraces had a multiple origin with a predonderance of Northern Flint germplasm for the two SWF groups, notably for the East part.
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Affiliation(s)
- Yacine Diaw
- Institut Sénégalais de Recherches Agricoles, ISRA-CNRA de Bambey, Dakar, Sénégal
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | | | - Alain Charcosset
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stéphane D. Nicolas
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Delphine Madur
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Joëlle Ronfort
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Jacques David
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Brigitte Gouesnard
- AGAP, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
- * E-mail:
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Natesan S, Singh TS, Duraisamy T, Chandrasekharan N, Chandran S, Adhimoolam K, Muniyandi SJ, Sampathrajan V, Kalipatty Nalliappan G, Muthurajan R, Meitei LJ. Characterization of crtRB1 Gene Polymorphism and β-Carotene Content in Maize Landraces Originated From North Eastern Himalayan Region (NEHR) of India. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Genetic diversity based on osmotic stress tolerance-related morpho-physiological traits and molecular markers in traditional rice cultivars. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00443-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Aci MM, Lupini A, Mauceri A, Morsli A, Khelifi L, Sunseri F. Genetic variation and structure of maize populations from Saoura and Gourara oasis in Algerian Sahara. BMC Genet 2018; 19:51. [PMID: 30068292 PMCID: PMC6090932 DOI: 10.1186/s12863-018-0655-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 07/12/2018] [Indexed: 11/14/2022] Open
Abstract
Background The ability of maize populations/landraces to tolerate drastically extreme environments over the past four centuries in Algeria leads to characterize these genetic resources for germplasm management as well as the identification of the best landraces useful for genetic improvement. Thus, the aim of the present work was a fingerprinting of an Algerian maize collection (47 landraces) from Saharan oasis by using 24 agro-morphological traits and18 Simple Sequence Repeats to evaluate genetic diversity and population structure. Results Phenotypic traits showed large significant variation in which earliness, plant size, ear and kernel features and crop yield appeared the most discriminant traits among landraces by using principal component analysis (PCA). One hundred ninety-seven different alleles were detected with a high mean number of allele per locus (10.9). The selected SSR were highly informative with PIC values > 0.65 as well as an overall genetic diversity (0.47) highlighting a broad genetic variability in the analyzed landraces. Genetic structure analysis revealed a high genetic differentiation among the 47 maize landraces with an overall Fst value (0.33). Cluster analysis for morphological traits as well as for SSR markers grouped the 47 Algerian populations regardless their geographic origin. Conclusions Maize from Algerian desert harbors a wide genetic diversity offering a source of novel/unique alleles useful for maize breeding programs to face the ongoing and future major challenge, the climate changes. Electronic supplementary material The online version of this article (10.1186/s12863-018-0655-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miyassa Meriem Aci
- LRGB, École Nationale Supérieure Agronomique (ENSA : ES1603), Avenue Pasteur, Hassan Badi, 16200, Algiers, El Harrach, Algeria
| | - Antonio Lupini
- Dipartimento AGRARIA, Università Mediterranea di Reggio Calabria, Località Feo di Vito snc, 89121, Reggio Calabria, Italy
| | - Antonio Mauceri
- Dipartimento AGRARIA, Università Mediterranea di Reggio Calabria, Località Feo di Vito snc, 89121, Reggio Calabria, Italy
| | - Abdelkader Morsli
- LRGB, École Nationale Supérieure Agronomique (ENSA : ES1603), Avenue Pasteur, Hassan Badi, 16200, Algiers, El Harrach, Algeria
| | - Lakhdar Khelifi
- LRGB, École Nationale Supérieure Agronomique (ENSA : ES1603), Avenue Pasteur, Hassan Badi, 16200, Algiers, El Harrach, Algeria.
| | - Francesco Sunseri
- Dipartimento AGRARIA, Università Mediterranea di Reggio Calabria, Località Feo di Vito snc, 89121, Reggio Calabria, Italy.
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Genomic-based-breeding tools for tropical maize improvement. Genetica 2017; 145:525-539. [PMID: 28875394 DOI: 10.1007/s10709-017-9981-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/14/2017] [Indexed: 10/18/2022]
Abstract
Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions. Heterosis breeding introduced in early 90 s improved maize yields significantly, but genetic gains is still a mirage, particularly for crop growing under marginal environments. Application of molecular markers has accelerated the pace of maize breeding to some extent. The availability of array of sequencing and genotyping technologies offers unrivalled service to improve precision in maize-breeding programs through modern approaches such as genomic selection, genome-wide association studies, bulk segregant analysis-based sequencing approaches, etc. Superior alleles underlying complex traits can easily be identified and introgressed efficiently using these sequence-based approaches. Integration of genomic tools and techniques with advanced genetic resources such as nested association mapping and backcross nested association mapping could certainly address the genetic issues in maize improvement programs in developing countries. Huge diversity in tropical maize and its inherent capacity for doubled haploid technology offers advantage to apply the next generation genomic tools for accelerating production in marginal environments of tropical and subtropical world. Precision in phenotyping is the key for success of any molecular-breeding approach. This article reviews genomic technologies and their application to improve agronomic traits in tropical maize breeding has been reviewed in detail.
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Sun X, Xie Y, Bi Y, Liu J, Amombo E, Hu T, Fu J. Comparative study of diversity based on heat tolerant-related morpho-physiological traits and molecular markers in tall fescue accessions. Sci Rep 2015; 5:18213. [PMID: 26666506 PMCID: PMC4678371 DOI: 10.1038/srep18213] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/09/2015] [Indexed: 11/28/2022] Open
Abstract
Heat stress is a critical challenge to tall fescue (Festuca arundinacea Schreb.) in many areas of the globe and variations in genetic structure and functional traits is for the efficient breeding programs on developing heat tolerant cultivars. Tolerant-related morpho-physiological traits and simple sequence repeat (SSR) markers were employed to survey genetic diversity in greenhouse and growth chamber trials. 100 tall fescue accessions, including 8 commercial cultivars and 92 natural genotypes, showed a high variation in phenotypic performance under heat stress. Based on standardized heat tolerant-related morpho-physiological data, all tall fescue accessions were clustered into five groups. The accessions with similar heat tolerance were likely to be clustered in the same group. The highest genetic diversity was obtained for accessions from Africa judged by Nei’s gene diversity (0.2640) and PIC (0.2112). All grass accessions could be divided into three major groups based on SSR markers, which was partially congruous to the geographical regions and history of introduction. A low correlation was found between morpho-physiological traits and SSR markers by Mantel test. The patterns in morpho-physiological trait variations and genetic diversity associated with heat tolerance were useful to design breeding programs for developing heat stress resistance in tall fescue.
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Affiliation(s)
- Xiaoyan Sun
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang 330096, China.,Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, Hubei, P.R. China
| | - Yan Xie
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, Hubei, P.R. China
| | - Yufang Bi
- Key Laboratory of High Efficent Processing of Bamboo, China National Bamboo Research Center, Hangzhou 310012, Zhejiang Province, China
| | - Jianping Liu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Erick Amombo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, Hubei, P.R. China
| | - Tao Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, Hubei, P.R. China
| | - Jinmin Fu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, Hubei, P.R. China
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Abstract
Maize (Zea mays L.) is not only of worldwide importance as a food, feed and as a source of diverse industrially important products, but is also a model genetic organism with immense genetic diversity. Although it was first domesticated in Mexico, maize landraces are widely found across the continents. Several studies in Mexico and other countries highlighted the genetic variability in the maize germplasm. Applications of molecular markers, particularly in the last two decades, have led to new insights into the patterns of genetic diversity in maize globally, including landraces as well as wild relatives (especially teosintes) in Latin America, helping in tracking the migration routes of maize from the centers of origin, and understanding the fate of genetic diversity during maize domestication. The genome sequencing of B73 (a highly popular US Corn Belt inbred) and Palomero (a popcorn landrace in Mexico) in the recent years are important landmarks in maize research, with significant implications to our understanding of the maize genome organization and evolution. Next-generation sequencing and high-throughput genotyping platforms promise to further revolutionize our understanding of genetic diversity and for designing strategies to utilize the genomic information for maize improvement. However, the major limiting factor to exploit the genetic diversity in crops like maize is no longer genotyping, but high-throughput and precision phenotyping. There is an urgent need to establish a global phenotyping network for comprehensive and efficient characterization of maize germplasm for an array of target traits, particularly for biotic and abiotic stress tolerance and nutritional quality. 'Seeds of Discovery' (SeeD), a novel initiative by CIMMYT with financial support from the Mexican Government for generating international public goods, has initiated intensive exploration of phenotypic and molecular diversity of maize germplasm conserved in the CIMMYT Gene Bank; this is expected to aid in effective identification and use of novel alleles and haplotypes for maize improvement. Multi-institutional efforts are required at the global level to systematically explore the maize germplasm to diversify the genetic base of elite breeding materials, create novel varieties and counter the effects of global climate changes.
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Affiliation(s)
- B M Prasanna
- International Maize and Wheat Improvement Center, Nairobi, Kenya.
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Wen W, Franco J, Chavez-Tovar VH, Yan J, Taba S. Genetic characterization of a core set of a tropical maize race Tuxpeño for further use in maize improvement. PLoS One 2012; 7:e32626. [PMID: 22412898 PMCID: PMC3296726 DOI: 10.1371/journal.pone.0032626] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 01/30/2012] [Indexed: 11/20/2022] Open
Abstract
The tropical maize race Tuxpeño is a well-known race of Mexican dent germplasm which has greatly contributed to the development of tropical and subtropical maize gene pools. In order to investigate how it could be exploited in future maize improvement, a panel of maize germplasm accessions was assembled and characterized using genome-wide Single Nucleotide Polymorphism (SNP) markers. This panel included 321 core accessions of Tuxpeño race from the International Maize and Wheat Improvement Center (CIMMYT) germplasm bank collection, 94 CIMMYT maize lines (CMLs) and 54 U.S. Germplasm Enhancement of Maize (GEM) lines. The panel also included other diverse sources of reference germplasm: 14 U.S. maize landrace accessions, 4 temperate inbred lines from the U.S. and China, and 11 CIMMYT populations (a total of 498 entries with 795 plants). Clustering analyses (CA) based on Modified Rogers Distance (MRD) clearly partitioned all 498 entries into their corresponding groups. No sub clusters were observed within the Tuxpeño core set. Various breeding strategies for using the Tuxpeño core set, based on grouping of the studied germplasm and genetic distance among them, were discussed. In order to facilitate sampling diversity within the Tuxpeño core, a minicore subset of 64 Tuxpeño accessions (20% of its usual size) representing the diversity of the core set was developed, using an approach combining phenotypic and molecular data. Untapped diversity represents further use of the Tuxpeño landrace for maize improvement through the core and/or minicore subset available to the maize community.
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Affiliation(s)
- Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Jorge Franco
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Suketoshi Taba
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
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Wang HW, Zhang B, Wang ZS, Cheng YQ, Ye YZ. Development and characterization of microsatellite loci in Taihangia rupestris (Rosaceae), a rare cliff herb. AMERICAN JOURNAL OF BOTANY 2010; 97:e136-e138. [PMID: 21616832 DOI: 10.3732/ajb.1000334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Microsatellite primers were developed for the rare Taihangia rupestris (Rosaceae) to evaluate genetic diversity, population genetic structure, mating system, and demographic events of this species. • METHODS AND RESULTS Ten primer sets were developed using an enriched genomic library and were successfully amplified in T. rupestris var. ciliata and T. rupestris var. rupestris. The number of alleles per locus ranged from 2 to 21; the observed and expected heterozygosities ranged from 0.300 to 0.950 and from 0.328 to 0.956, respectively, in the two varieties. • CONCLUSIONS The markers described here will be useful for studies of genetic variation, genetic structure, and mating systems of T. rupestris, which are important for the future conservation of this rare species.
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Affiliation(s)
- Hong-Wei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
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