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Yahaya MA, Shimelis H, Nebie B, Ojiewo CO, Rathore A, Das R. Genetic Diversity and Population Structure of African Sorghum ( Sorghum bicolor L. Moench) Accessions Assessed through Single Nucleotide Polymorphisms Markers. Genes (Basel) 2023; 14:1480. [PMID: 37510384 PMCID: PMC10379961 DOI: 10.3390/genes14071480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Assessing the genetic diversity and population structure of cultivated sorghum is important for heterotic grouping, breeding population development, marker-assisted cultivar development, and release. The objectives of the present study were to assess the genetic diversity and deduce the population structure of 200 sorghum accessions using diversity arrays technology (DArT)-derived single nucleotide polymorphism (SNP) markers. The expected heterozygosity values ranged from 0.10 to 0.50 with an average of 0.32, while the average observed heterozygosity (0.15) was relatively low, which is a typical value for autogamous crops species like sorghum. Moderate polymorphic information content (PIC) values were identified with a mean of 0.26, which indicates the informativeness of the chosen SNP markers. The population structure and cluster analyses revealed four main clusters with a high level of genetic diversity among the accessions studied. The variation within populations (41.5%) was significantly higher than that among populations (30.8%) and between samples within the structure (27.7%). The study identified distantly related sorghum accessions such as SAMSORG 48, KAURA RED GLUME; Gadam, AS 152; CSRO1, ICNSL2014-062; and YALAI, KAFI MORI. The accessions exhibited wide genetic diversity that will be useful in developing new gene pools and novel genotypes for West Africa sorghum breeding programs.
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Affiliation(s)
- Muhammad Ahmad Yahaya
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
- Department of Plant Science, Institute for Agricultural Research Samaru, Ahmadu Bello University Zaria, PMB 1044, Kaduna 810211, Nigeria
| | - Hussein Shimelis
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
| | - Baloua Nebie
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 3320, Escale Thiès BP 3320, Senegal
| | - Chris Ochieng Ojiewo
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041, Nairobi 00621, Kenya
| | - Abhishek Rathore
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041, Nairobi 00621, Kenya
| | - Roma Das
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041, Nairobi 00621, Kenya
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Adedugba AA, Adeyemo OA, Adetumbi AJ, Amusa OD, Ogunkanmi LA. Evaluation of genetic variability for major agro-morphological and stalk sugar traits in African sorghum genotypes. Heliyon 2023; 9:e14622. [PMID: 36994400 PMCID: PMC10040710 DOI: 10.1016/j.heliyon.2023.e14622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/22/2023] Open
Abstract
The study aimed to assess one hundred and twelve (112) accessions of sorghum sourced from Nigeria and other four African countries for their genetic variability, heritability (broad sense) and genetic advance components to identify promising accessions with high grain yield and sweet stalk which can serve as future parents for breeding dual-purpose lines. The accessions were evaluated at Ilora, Oyo State, Nigeria in a randomized complete block design (RCBD) layout with three replicates in two planting seasons (2020 and 2021). The results showed that the phenotypic coefficient of variation (PCV) was higher than the genotypic coefficient of variation (GCV). The highest PCV and GCV were grain yield (51.89%) and inflorescence length (42.26%), respectively, while a hundred seed grain weight had the lowest PCV (17.83%) and GCV (21.55%). The range of genetic advance over mean (GAM) was 28.33% for leaf width and 81.62% for inflorescence length. Inflorescence length had the highest values of heritability and GAM (0.88, 81.62%), while a low value was obtained for grain yield (0.27, 29.32%). Twenty-two accessions had higher grain yields than the yields of check varieties. The high-yielding accessions, SG57, SG31, SG06, and SG12 had grain yields of 3.07 t/ha, 2.89 t/ha, 2.76 t/ha and 2.73 t/ha, respectively. Fourteen accessions had wet stalks, of which 12 of the accessions had soluble stalk sugar (Brix) above 12%, which is comparable to the amount found in sweet sorghum. Three accessions with Brix above 12% (SG16, SG31, SG32) and high grain yields (2.32 t/ha, 2.89 t/ha and 2.02 t/ha) were identified as promising accessions. There is considerable genetic diversity among African sorghum accessions in Nigeria's southwest agroecosystem, which should improve food security and breeding potential.
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Keivani M, Mehregan I, Albach DC. Evaluating morphological diversity among Plantago major L. populations and influence of ecological variables. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00711-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Rashid M, Yousaf Z, Ullah MN, Munawar M, Riaz N, Younas A, Aftab A, Shamsheer B. Genetic variability assessment of worldwide spinach accessions by agro-morphological traits. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2020. [DOI: 10.1080/16583655.2020.1853920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Madiha Rashid
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
- Department of Botany, University of Education, Township Campus, Lahore, Pakistan
- Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Zubaida Yousaf
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Muhammad Najeeb Ullah
- Vegetable Research Institute, Ayub Agriculture Research Institute, Faisalabad, Pakistan
| | - Muneeb Munawar
- Vegetable Research Institute, Ayub Agriculture Research Institute, Faisalabad, Pakistan
| | - Nadia Riaz
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Arusa Aftab
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Bushra Shamsheer
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
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Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum ( Sorghum bicolor). Genetics 2019; 211:1075-1087. [PMID: 30622134 PMCID: PMC6404259 DOI: 10.1534/genetics.118.301742] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/22/2018] [Indexed: 11/18/2022] Open
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a major staple food cereal for millions of people worldwide. Valluru et al. identify putative deleterious mutations among ∼5.5M segregating variants of 229 diverse sorghum... Sorghum (Sorghum bicolor L.) is a major food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. The lack of recombination, drift, and the coupling with favorable loci impede the removal of deleterious mutations from the genome by selection. To study how deleterious variants impact phenotypes, we identified putative deleterious mutations among ∼5.5 M segregating variants of 229 diverse biomass sorghum lines. We provide the whole-genome estimate of the deleterious burden in sorghum, showing that ∼33% of nonsynonymous substitutions are putatively deleterious. The pattern of mutation burden varies appreciably among racial groups. Across racial groups, the mutation burden correlated negatively with biomass, plant height, specific leaf area (SLA), and tissue starch content (TSC), suggesting that deleterious burden decreases trait fitness. Putatively deleterious variants explain roughly one-half of the genetic variance. However, there is only moderate improvement in total heritable variance explained for biomass (7.6%) and plant height (average of 3.1% across all stages). There is no advantage in total heritable variance for SLA and TSC. The contribution of putatively deleterious variants to phenotypic diversity therefore appears to be dependent on the genetic architecture of traits. Overall, these results suggest that incorporating putatively deleterious variants into genomic models slightly improves prediction accuracy because of extensive linkage. Knowledge of deleterious variants could be leveraged for sorghum breeding through either genome editing and/or conventional breeding that focuses on the selection of progeny with fewer deleterious alleles.
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Olatoye MO, Hu Z, Maina F, Morris GP. Genomic Signatures of Adaptation to a Precipitation Gradient in Nigerian Sorghum. G3 (BETHESDA, MD.) 2018; 8:3269-3281. [PMID: 30097471 PMCID: PMC6169398 DOI: 10.1534/g3.118.200551] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/04/2018] [Indexed: 02/05/2023]
Abstract
Evolution of plants under climatic gradients may lead to clinal adaptation. Understanding the genomic basis of clinal adaptation in crops species could facilitate breeding for climate resilience. We investigated signatures of clinal adaptation in the cereal crop sorghum (Sorghum bicolor L. [Moench]) to the precipitation gradient in West Africa using a panel (n = 607) of sorghum accessions from diverse agroclimatic zones of Nigeria. Significant correlations were observed between common-garden phenotypes of three putative climate-adaptive traits (flowering time, plant height, and panicle length) and climatic variables. The panel was characterized at >400,000 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). Redundancy analysis indicated that a small proportion of SNP variation can be explained by climate (1%), space (1%), and climate collinear with space (3%). Discriminant analysis of principal components identified three genetic groups that are distributed differently along the precipitation gradient. Genome-wide association studies were conducted with phenotypes and three climatic variables (annual mean precipitation, precipitation in the driest quarter, and annual mean temperature). There was no overall enrichment of associations near a priori candidate genes implicated in flowering time, height, and inflorescence architecture in cereals, but several significant associations were found near a priori candidates including photoperiodic flowering regulators SbCN12 and Ma6 Together, the findings suggest that a small (3%) but significant proportion of nucleotide variation in Nigerian sorghum landraces reflects clinal adaptation along the West African precipitation gradient.
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Affiliation(s)
- Marcus O Olatoye
- Department of Agronomy, Kansas State University, Manhattan KS 66506
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan KS 66506
| | - Fanna Maina
- Department of Agronomy, Kansas State University, Manhattan KS 66506
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Maina F, Bouchet S, Marla SR, Hu Z, Wang J, Mamadou A, Abdou M, Saïdou AA, Morris GP. Population genomics of sorghum (Sorghum bicolor) across diverse agroclimatic zones of Niger. Genome 2018; 61:223-232. [PMID: 29432699 DOI: 10.1139/gen-2017-0131] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed 516 Nigerien accessions for which local variety name, botanical race, and geographic origin were known. We discovered 144 299 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). We performed discriminant analysis of principal components (DAPC), which identified six genetic groups, and performed a genome scan for loci with high discriminant loadings. The highest discriminant coefficients were on chromosome 9, near the putative ortholog of maize flowering time adaptation gene Vgt1. Next, we characterized differentiation among local varieties and used a genome scan of pairwise FST values to identify SNPs associated with specific local varieties. Comparison of varieties named for light- versus dark-grain identified differentiation near Tannin1, the major gene responsible for grain tannins. These findings could facilitate genomics-assisted breeding of locally adapted and farmer-preferred sorghum varieties for Niger.
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Affiliation(s)
- Fanna Maina
- a Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA.,b Institut National de la Recherche Agronomique du Niger (INRAN) Niamey, Niger
| | - Sophie Bouchet
- c Institut National de la Recherche Agronomique (INRA), l'Université Clermont Auvergne (UCA), 63000 Clermont-Ferrand, France
| | - Sandeep R Marla
- a Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Zhenbin Hu
- a Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Jianan Wang
- a Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Aissata Mamadou
- b Institut National de la Recherche Agronomique du Niger (INRAN) Niamey, Niger
| | - Magagi Abdou
- d La Sahelienne Des Semences HALAL, Maradi, Niger
| | | | - Geoffrey P Morris
- a Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
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De Luca D, Cennamo P, Del Guacchio E, Di Novella R, Caputo P. Conservation and genetic characterisation of common bean landraces from Cilento region (southern Italy): high differentiation in spite of low genetic diversity. Genetica 2017; 146:29-44. [PMID: 29030763 DOI: 10.1007/s10709-017-9994-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/25/2017] [Indexed: 11/26/2022]
Abstract
Since its introduction from Central-South America to Italy almost 500 years ago, the common bean (Phaseolus vulgaris L.) was largely cultivated across the peninsula in hundreds of different landraces. However, globalisation and technological modernisation of agricultural practices in the last decades promoted the cultivation of few varieties at the expense of traditional and local agro-ecotypes, which have been confined to local markets or have completely disappeared. The aim of this study was to evaluate the genetic diversity and differentiation in 12 common bean landraces once largely cultivated in the Cilento region (Campania region, southern Italy), and now the object of a recovery program to save them from extinction. The analysis conducted using 13 nuclear microsatellite loci in 140 individuals revealed a high degree of homozygosity within each landrace and a strong genetic differentiation that was reflected in the success in assigning individuals to the source landrace. On the contrary, internal transcribed spacers 1 and 2, analysed in one individual per landrace, were highly similar among common bean landraces but allowed the identification of a cowpea variety (Vigna unguiculata Walp.), a crop largely cultivated in the Old World before the arrival of common bean from Americas. In conclusion, our study highlighted that conservation of landraces is important not only for the cultural and socio-economic value that they have for local communities, but also because the time and conditions in which they have been selected have led to that genetic distinctiveness that is at the basis of many potential agronomical applications and dietary benefits.
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Affiliation(s)
- Daniele De Luca
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, via Foria 223, 80139, Naples, Italy.
| | - Paola Cennamo
- Facoltà di Lettere, Università degli Studi Suor Orsola Benincasa di Napoli, Via Santa Caterina da Siena 37, 80135, Naples, Italy
| | - Emanuele Del Guacchio
- Facoltà di Scienze della Formazione, Università degli Studi Suor Orsola Benincasa di Napoli, Via Santa Caterina da Siena 37, 80135, Naples, Italy
| | | | - Paolo Caputo
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, via Foria 223, 80139, Naples, Italy
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Ranwez V, Serra A, Pot D, Chantret N. Domestication reduces alternative splicing expression variations in sorghum. PLoS One 2017; 12:e0183454. [PMID: 28886042 PMCID: PMC5590825 DOI: 10.1371/journal.pone.0183454] [Citation(s) in RCA: 7] [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: 04/19/2017] [Accepted: 08/06/2017] [Indexed: 01/09/2023] Open
Abstract
Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum accessions (ten accessions for each pool). In that aim, we focus on genes expressing two isoforms in sorghum and estimate the ratio between expression levels of those isoforms in each accession. Noticeably, for a given gene, one isoform can either be overexpressed or underexpressed in some wild accessions, whereas in the cultivated accessions, the balance between the two isoforms of the same gene appears to be much more homogenous. Indeed, we observe in sorghum significantly more variation in isoform expression balance among wild accessions than among domesticated accessions. The possibility exists that the loss of nucleotide diversity due to domestication could affect regulatory elements, controlling transcription or degradation of these isoforms. Impact on the isoform expression balance is discussed. As far as we know, this is the first time that the impact of domestication on transcript isoform balance has been studied at the genomic scale. This could pave the way towards the identification of key domestication genes with finely tuned isoform expressions in domesticated accessions while being highly variable in their wild relatives.
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Affiliation(s)
| | - Audrey Serra
- Montpellier SupAgro, UMR AGAP, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Montpellier, France
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da Silva MJ, Pastina MM, de Souza VF, Schaffert RE, Carneiro PCS, Noda RW, Carneiro JEDS, Damasceno CMB, Parrella RADC. Phenotypic and molecular characterization of sweet sorghum accessions for bioenergy production. PLoS One 2017; 12:e0183504. [PMID: 28817696 PMCID: PMC5560702 DOI: 10.1371/journal.pone.0183504] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/04/2017] [Indexed: 11/18/2022] Open
Abstract
Sweet sorghum [Sorghum bicolor (L.) Moench] is a type of cultivated sorghum characterized by the accumulation of high levels of sugar in the stems and high biomass accumulation, making this crop an important feedstock for bioenergy production. Sweet sorghum breeding programs that focus on bioenergy have two main goals: to improve quantity and quality of sugars in the juicy stem and to increase fresh biomass productivity. Genetic diversity studies are very important for the success of a breeding program, especially in the early stages, where understanding the genetic relationship between accessions is essential to identify superior parents for the development of improved breeding lines. The objectives of this study were: to perform phenotypic and molecular characterization of 100 sweet sorghum accessions from the germplasm bank of the Embrapa Maize and Sorghum breeding program; to examine the relationship between the phenotypic and the molecular diversity matrices; and to infer about the population structure in the sweet sorghum accessions. Morphological and agro-industrial traits related to sugar and biomass production were used for phenotypic characterization, and single nucleotide polymorphisms (SNPs) were used for molecular diversity analysis. Both phenotypic and molecular characterizations revealed the existence of considerable genetic diversity among the 100 sweet sorghum accessions. The correlation between the phenotypic and the molecular diversity matrices was low (0.35), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and the molecular diversity analyses. Furthermore, the clusters obtained by the molecular diversity analysis were more consistent with the genealogy and the historic background of the sweet sorghum accessions than the clusters obtained through the phenotypic diversity analysis. The low correlation observed between the molecular and the phenotypic diversity matrices highlights the complementarity between the molecular and the phenotypic characterization to assist a breeding program.
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Affiliation(s)
- Michele Jorge da Silva
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brasil
| | | | - Vander Fillipe de Souza
- Departamento de Engenharia de Biossistemas, Universidade Federal de São João del-Rei, São João del-Rei, Minas Gerais, Brasil
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Sinha S, Kumaravadivel N. Understanding Genetic Diversity of Sorghum Using Quantitative Traits. SCIENTIFICA 2016; 2016:3075023. [PMID: 27382499 PMCID: PMC4921636 DOI: 10.1155/2016/3075023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 05/17/2016] [Indexed: 05/09/2023]
Abstract
Sorghum is the important cereal crop around the world and hence understanding and utilizing the genetic variation in sorghum accessions are essential for improving the crop. A good understanding of genetic variability among the accessions will enable precision breeding. So profiling the genetic diversity of sorghum is imminent. In the present investigation, forty sorghum accessions consisting of sweet sorghum, grain sorghum, forage sorghum, mutant lines, maintainer lines, and restorer lines were screened for genetic diversity using quantitative traits. Observations were recorded on 14 quantitative traits, out of which 9 diverse traits contributing to maximum variability were selected for genetic diversity analysis. The principle component analysis revealed that the panicle width, stem girth, and leaf breadth contributed maximum towards divergence. By using hierarchical cluster analysis, the 40 accessions were grouped under 6 clusters. Cluster I contained maximum number of accessions and cluster VI contained the minimum. The maximum intercluster distance was observed between cluster VI and cluster IV. Cluster III had the highest mean value for hundred-seed weight and yield. Hence the selection of parents must be based on the wider intercluster distance and superior mean performance for yield and yield components. Thus in the present investigation quantitative data were able to reveal the existence of a wide genetic diversity among the sorghum accessions used providing scope for further genetic improvement.
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Affiliation(s)
- Sweta Sinha
- Department of Plant Molecular Biology and Biotechnology, Centre for Plant Molecular Biology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003, India
- *Sweta Sinha:
| | - N. Kumaravadivel
- Department of Plant Molecular Biology and Biotechnology, Centre for Plant Molecular Biology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003, India
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Zhang QD, Jia RZ, Meng C, Ti CW, Wang YL. Diversity and population structure of a dominant deciduous tree based on morphological and genetic data. AOB PLANTS 2015; 7:plv103. [PMID: 26311734 PMCID: PMC4621740 DOI: 10.1093/aobpla/plv103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/27/2015] [Indexed: 06/04/2023]
Abstract
Knowledge of the genetic diversity and structure of tree species across their geographic ranges is essential for sustainable use and management of forest ecosystems. Acer grosseri Pax., an economically and ecologically important maple species, is mainly distributed in North China. In this study, the genetic diversity and population differentiation of 24 natural populations of this species were evaluated using sequence-related amplified polymorphism markers and morphological characters. The results show that highly significant differences occurred in 32 morphological traits. The coefficient of variation of 34 characters was 18.19 %. Principal component analysis indicated that 18 of 34 traits explained 60.20 % of the total variance. The phenotypic differentiation coefficient (VST) was 36.06 % for all morphological traits. The Shannon-Wiener index of 34 morphological characters was 6.09, while at the population level, it was 1.77. The percentage of polymorphic bands of all studied A. grosseri populations was 82.14 %. Nei's gene diversity (He) and Shannon's information index (I) were 0.35 and 0.50, respectively. Less genetic differentiation was detected among the natural populations (GST = 0.20, ΦST = 0.10). Twenty-four populations of A. grosseri formed two main clusters, which is consistent with morphological cluster analysis. Principal coordinates analysis and STRUCTURE analysis supported the UPGMA-cluster dendrogram. There was no significant correlation between genetic and geographical distances among populations. Both molecular and morphological data suggested that A. grosseri is rich in genetic diversity. The high level of genetic variation within populations could be affected by the biological characters, mating system and lifespan of A. grosseri, whereas the lower genetic diversity among populations could be caused by effective gene exchange, selective pressure from environmental heterogeneity and the species' geographical range.
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Affiliation(s)
- Qin-di Zhang
- College of Life Sciences, Shanxi Normal University, Linfen 041000, China
| | - Rui-Zhi Jia
- College of Life Sciences, Shanxi Normal University, Linfen 041000, China
| | - Chao Meng
- College of Life Sciences, Shanxi Normal University, Linfen 041000, China
| | - Chao-Wen Ti
- College of Life Sciences, Shanxi Normal University, Linfen 041000, China
| | - Yi-Ling Wang
- College of Life Sciences, Shanxi Normal University, Linfen 041000, China
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Assessment of genetic diversity among sorghum landraces and their wild/weedy relatives in western Kenya using simple sequence repeat (SSR) markers. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0616-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Leiser WL, Rattunde HFW, Weltzien E, Cisse N, Abdou M, Diallo A, Tourè AO, Magalhaes JV, Haussmann BIG. Two in one sweep: aluminum tolerance and grain yield in P-limited soils are associated to the same genomic region in West African sorghum. BMC PLANT BIOLOGY 2014; 14:206. [PMID: 25112843 PMCID: PMC4256928 DOI: 10.1186/s12870-014-0206-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 07/22/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Sorghum (Sorghum bicolor L. Moench) productivity is severely impeded by low phosphorus (P) and aluminum (Al) toxic soils in sub-Saharan Africa and especially West Africa (WA). Improving productivity of this staple crop under these harsh conditions is crucial to improve food security and farmer's incomes in WA. RESULTS This is the first study to examine the genetics underlying sorghum adaptation to phosphorus limitation in a wide range of WA growing conditions. A set of 187 diverse sorghum genotypes were grown in 29 -P and + P field experiments from 2006-2012 in three WA countries. Sorghum grain yield performance under -P and + P conditions was highly correlated (r = 0.85***). Significant genotype-by-phosphorus interaction was detected but with small magnitude compared to the genotype variance component. We observed high genetic diversity within our panel, with rapid linkage disequilibrium decay, confirming recent sequence based studies in sorghum. Using genome wide association mapping based on 220 934 SNPs we identified one genomic region on chromosome 3 that was highly associated to grain yield production. A major Al-tolerance gene in sorghum, SbMATE, was collocated in this region and SbMATE specific SNPs showed very high associations to grain yield production, especially under -P conditions, explaining up to 16% of the genotypic variance. CONCLUSION The results suggest that SbMATE has a possible pleiotropic role in providing tolerance to two of the most serious abiotic stresses for sorghum in WA, Al toxicity and P deficiency. The identified SNPs can help accelerate breeding for increased sorghum productivity under unfavorable soil conditions and contribute to assuring food security in WA.
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Affiliation(s)
- Willmar L Leiser
- />Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany
- />International Crops Research Institute for the Semi-Arid Tropics, P 320, Bamako, Mali
| | | | - Eva Weltzien
- />International Crops Research Institute for the Semi-Arid Tropics, P 320, Bamako, Mali
| | - Ndiaga Cisse
- />Institut Sénégalais de Recherches Agricoles, BP 3320, Thiès, Senegal
| | - Magagi Abdou
- />Institut National de la Recherche Agronomique, CERRA de Maradi, BP 240, Maradi, Niger
| | | | | | - Jurandir V Magalhaes
- />Embrapa Maize and Sorghum, Rod. MG 424, Km 65, 35701-970 Sete Lagoas, Minas Gerais Brazil
| | - Bettina IG Haussmann
- />Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany
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15
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Gupta S, Kumari K, Muthamilarasan M, Parida SK, Prasad M. Population structure and association mapping of yield contributing agronomic traits in foxtail millet. PLANT CELL REPORTS 2014; 33:881-93. [PMID: 24413764 DOI: 10.1007/s00299-014-1564-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 12/06/2013] [Accepted: 12/31/2013] [Indexed: 05/20/2023]
Abstract
Association analyses accounting for population structure and relative kinship identified eight SSR markers ( p < 0.01) showing significant association ( R (2) = 18 %) with nine agronomic traits in foxtail millet. Association mapping is an efficient tool for identifying genes regulating complex traits. Although association mapping using genomic simple sequence repeat (SSR) markers has been successfully demonstrated in many agronomically important crops, very few reports are available on marker-trait association analysis in foxtail millet. In the present study, 184 foxtail millet accessions from diverse geographical locations were genotyped using 50 SSR markers representing the nine chromosomes of foxtail millet. The genetic diversity within these accessions was examined using a genetic distance-based and a general model-based clustering method. The model-based analysis using 50 SSR markers identified an underlying population structure comprising five sub-populations which corresponded well with distance-based groupings. The phenotyping of plants was carried out in the field for three consecutive years for 20 yield contributing agronomic traits. The linkage disequilibrium analysis considering population structure and relative kinship identified eight SSR markers (p < 0.01) on different chromosomes showing significant association (R (2) = 18 %) with nine agronomic traits. Four of these markers were associated with multiple traits. The integration of genetic and physical map information of eight SSR markers with their functional annotation revealed strong association of two markers encoding for phospholipid acyltransferase and ubiquitin carboxyl-terminal hydrolase located on the same chromosome (5) with flag leaf width and grain yield, respectively. Our findings on association mapping is the first report on Indian foxtail millet germplasm and this could be effectively applied in foxtail millet breeding to further uncover marker-trait associations with a large number of markers.
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Affiliation(s)
- Sarika Gupta
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, JNU Campus, New Delhi, 110 067, India
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16
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Adugna A. Analysis of in situ diversity and population structure in Ethiopian cultivated Sorghum bicolor (L.) landraces using phenotypic traits and SSR markers. SPRINGERPLUS 2014; 3:212. [PMID: 24877027 PMCID: PMC4033718 DOI: 10.1186/2193-1801-3-212] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 04/23/2014] [Indexed: 01/16/2023]
Abstract
Genetic diversity is a fundamental input for every plant breeding program, genetic resources conservation, and evolutionary studies. In situ diversity and population genetic structure of eight cultivated sorghum landrace populations were investigated in the center of origin, Ethiopia using seven phenotypic traits and 12 highly polymorphic sorghum SSR markers. In farmers' fields, DNA samples were collected using Whatman® plant saver card and quantitative phenotypic traits were measured from 160 individual plant samples belonging to the eight populations representing three diverse geographical regions. High diversity was observed among the various populations for the measured phenotypic traits. The 12 SSR loci produced a total of 123 alleles of which 78 (63.41%) were rare (frequency ≤0.05) with an average of 10.25 alleles per polymorphic locus. The polymorphism information content (PIC) was in the range 0.39-0.85 showing the good discriminatory power of the SSR loci used. Average observed heterozygosity and gene diversity across all populations and loci ranged 0.04-0.33 and 0.41-0.87, respectively. Neighbor-joining and STRUCTURE analyses grouped the 160 samples from the eight populations differently. AMOVA showed 54.44% of the variation to be within populations, 32.76% among populations within regions, and 12.8% among the regions of origin. There was high divergence in the total populations (FST = 0.40) indicating low level of gene flow (Nm = 0.38), but high gene flow was also observed in some adjacent populations. The populations from Wello displayed close relationship with remote Gibe and Metekel populations indicating that the variation followed human migration patterns. Implications of the results for sorghum improvement and germplasm conservation are discussed.
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Affiliation(s)
- Asfaw Adugna
- Melkassa Agricultural Research Center, P.O. Box 1085, Adama, Ethiopia
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17
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Ramu P, Billot C, Rami JF, Senthilvel S, Upadhyaya HD, Ananda Reddy L, Hash CT. Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2051-64. [PMID: 23708149 DOI: 10.1007/s00122-013-2117-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 05/08/2013] [Indexed: 05/09/2023]
Abstract
Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379-0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping.
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Affiliation(s)
- P Ramu
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Andhra Pradesh, India.
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18
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Genetic diversity and population structure of Chinese foxtail millet [Setaria italica (L.) Beauv.] landraces. G3-GENES GENOMES GENETICS 2012; 2:769-77. [PMID: 22870400 PMCID: PMC3385983 DOI: 10.1534/g3.112.002907] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 05/03/2012] [Indexed: 01/07/2023]
Abstract
As an ancient cereal of great importance for dryland agriculture even today, foxtail millet (Setaria italica) is fast becoming a new plant genomic model crop. A genotypic analysis of 250 foxtail millet landraces, which represent 1% of foxtail millet germplasm kept in the Chinese National Gene Bank (CNGB), was conducted with 77 SSRs covering the foxtail millet genome. A high degree of molecular diversity among the landraces was found, with an average of 20.9 alleles per locus detected. STRUCTURE, neighbor-jointing, and principal components analyses classify the accessions into three clusters (topmost hierarchy) and, ultimately, four conservative subgroups (substructuring within the topmost clusters) in total, which are in good accordance with eco-geographical distribution in China. The highest subpopulation diversity was identified in the accessions of Pop3 from the middle regions of the Yellow River, followed by accessions in Pop1 from the downstream regions of the Yellow River, suggesting that foxtail millet was domesticated in the Yellow River drainage area first and then spread to other parts of the country. Linkage disequilibrium (LD) decay of less than 20 cM of genetic distance in the foxtail millet landrace genome was observed, which suggests that it could be possible to achieve resolution down to the 20 cM level for association mapping.
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19
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Social Organization of Crop Genetic Diversity. The G × E × S Interaction Model. DIVERSITY-BASEL 2011. [DOI: 10.3390/d4010001] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Sagnard F, Deu M, Dembélé D, Leblois R, Touré L, Diakité M, Calatayud C, Vaksmann M, Bouchet S, Mallé Y, Togola S, Traoré PCS. Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild-weedy-crop complex in a western African region. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1231-46. [PMID: 21811819 DOI: 10.1007/s00122-011-1662-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 07/09/2011] [Indexed: 05/08/2023]
Abstract
Gene flow between domesticated plants and their wild relatives is one of the major evolutionary processes acting to shape their structure of genetic diversity. Earlier literature, in the 1970s, reported on the interfertility and the sympatry of wild, weedy and cultivated sorghum belonging to the species Sorghum bicolor in most regions of sub-Saharan Africa. However, only a few recent surveys have addressed the geographical and ecological distribution of sorghum wild relatives and their genetic structure. These features are poorly documented, especially in western Africa, a centre of diversity for this crop. We report here on an exhaustive in situ collection of wild, weedy and cultivated sorghum assembled in Mali and in Guinea. The extent and pattern of genetic diversity were assessed with 15 SSRs within the cultivated pool (455 accessions), the wild pool (91 wild and weedy forms) and between them. F (ST) and R (ST) statistics, distance-based trees, Bayesian clustering methods, as well as isolation by distance models, were used to infer evolutionary relationships within the wild-weedy-crop complex. Firstly, our analyses highlighted a strong racial structure of genetic diversity within cultivated sorghum (F (ST) = 0.40). Secondly, clustering analyses highlighted the introgressed nature of most of the wild and weedy sorghum and grouped them into two eco-geographical groups. Such closeness between wild and crop sorghum could be the result of both sorghum's domestication history and preferential post-domestication crop-to-wild gene flow enhanced by farmers' practices. Finally, isolation by distance analyses showed strong spatial genetic structure within each pool, due to spatially limited dispersal, and suggested consequent gene flow between the wild and the crop pools, also supported by R (ST) analyses. Our findings thus revealed important features for the collection, conservation and biosafety of domesticated and wild sorghum in their centre of diversity.
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Affiliation(s)
- Fabrice Sagnard
- CIRAD, UMR AGAP, Avenue d'Agropolis, 34398, Montpellier, France
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21
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Odong TL, van Heerwaarden J, Jansen J, van Hintum TJL, van Eeuwijk FA. Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data? TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:195-205. [PMID: 21472410 PMCID: PMC3114091 DOI: 10.1007/s00122-011-1576-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 03/18/2011] [Indexed: 05/04/2023]
Abstract
Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies.
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Affiliation(s)
- T L Odong
- Wageningen University and Research, Biometris, Wageningen, The Netherlands.
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22
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Mutegi E, Sagnard F, Semagn K, Deu M, Muraya M, Kanyenji B, de Villiers S, Kiambi D, Herselman L, Labuschagne M. Genetic structure and relationships within and between cultivated and wild sorghum (Sorghum bicolor (L.) Moench) in Kenya as revealed by microsatellite markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:989-1004. [PMID: 21153801 DOI: 10.1007/s00122-010-1504-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 11/22/2010] [Indexed: 05/30/2023]
Abstract
Understanding the extent and partitioning of diversity within and among crop landraces and their wild/weedy relatives constitutes the first step in conserving and unlocking their genetic potential. This study aimed to characterize the genetic structure and relationships within and between cultivated and wild sorghum at country scale in Kenya, and to elucidate some of the underlying evolutionary mechanisms. We analyzed at total of 439 individuals comprising 329 cultivated and 110 wild sorghums using 24 microsatellite markers. We observed a total of 295 alleles across all loci and individuals, with 257 different alleles being detected in the cultivated sorghum gene pool and 238 alleles in the wild sorghum gene pool. We found that the wild sorghum gene pool harbored significantly more genetic diversity than its domesticated counterpart, a reflection that domestication of sorghum was accompanied by a genetic bottleneck. Overall, our study found close genetic proximity between cultivated sorghum and its wild progenitor, with the extent of crop-wild divergence varying among cultivation regions. The observed genetic proximity may have arisen primarily due to historical and/or contemporary gene flow between the two congeners, with differences in farmers' practices explaining inter-regional gene flow differences. This suggests that deployment of transgenic sorghum in Kenya may lead to escape of transgenes into wild-weedy sorghum relatives. In both cultivated and wild sorghum, genetic diversity was found to be structured more along geographical level than agro-climatic level. This indicated that gene flow and genetic drift contributed to shaping the contemporary genetic structure in the two congeners. Spatial autocorrelation analysis revealed a strong spatial genetic structure in both cultivated and wild sorghums at the country scale, which could be explained by medium- to long-distance seed movement.
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Affiliation(s)
- E Mutegi
- Kenya Agricultural Research Institute (KARI), National Genebank, Nairobi, Kenya.
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