1
|
Adu GB, Awuku FJ, Garcia-Oliveira AL, Amegbor IK, Nelimor C, Nboyine J, Karikari B, Atosona B, Manigben KA, Aboyadana PA. DArTseq-based SNP markers reveal high genetic diversity among early generation fall armyworm tolerant maize inbred lines. PLoS One 2024; 19:e0294863. [PMID: 38630672 PMCID: PMC11023204 DOI: 10.1371/journal.pone.0294863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/09/2023] [Indexed: 04/19/2024] Open
Abstract
Diversity analysis using molecular markers serves as a powerful tool in unravelling the intricacies of inclusivity within various populations and is an initial step in the assessment of populations and the development of inbred lines for host plant resistance in maize. This study was conducted to assess the genetic diversity and population structure of 242 newly developed S3 inbred lines using 3,305 single nucleotide polymorphism (SNP) markers and to also assess the level of homozygosity achieved in each of the inbred lines. A total of 1,184 SNP markers were found highly informative, with a mean polymorphic information content (PIC) of 0.23. Gene diversity was high among the inbred lines, ranging from 0.04 to 0.50, with an average of 0.27. The residual heterozygosity of the 242 S3 inbred lines averaged 8.8%, indicating moderately low heterozygosity levels among the inbred lines. Eighty-four percent of the 58,322 pairwise kinship coefficients among the inbred lines were near zero (0.00-0.05), with only 0.3% of them above 0.50. These results revealed that many of the inbred lines were distantly related, but none were redundant, suggesting each inbred line had a unique genetic makeup with great potential to provide novel alleles for maize improvement. The admixture-based structure analysis, principal coordinate analysis, and neighbour-joining clustering were concordant in dividing the 242 inbred lines into three subgroups based on the pedigree and selection history of the inbred lines. These findings could guide the effective use of the newly developed inbred lines and their evaluation in quantitative genetics and molecular studies to identify candidate lines for breeding locally adapted fall armyworm tolerant varieties in Ghana and other countries in West and Central Africa.
Collapse
Affiliation(s)
| | | | - Ana Luisa Garcia-Oliveira
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
- Department of Molecular Biology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, Haryana, India
| | - Isaac Kodzo Amegbor
- CSIR-Savanna Agricultural Research Institute, Nyankpala, Ghana
- Faculty of Natural and Agricultural Sciences, Department of Plant Breeding, University of the Free State, Bloemfontein, South Africa
| | - Charles Nelimor
- CSIR-Savanna Agricultural Research Institute, Nyankpala, Ghana
| | - Jerry Nboyine
- CSIR-Savanna Agricultural Research Institute, Nyankpala, Ghana
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | | | | | | |
Collapse
|
2
|
Beaton K, Mazadza A, Chikwambi Z. Identification of Zimbabwe's locally grown banana (Musa Spp.) cultivars using morphology and genome-targeted sequencing. J Genet Eng Biotechnol 2023; 21:118. [PMID: 37962722 PMCID: PMC10646137 DOI: 10.1186/s43141-023-00562-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/13/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Banana production is increasingly under threat due to harsh weather conditions as a result of climate change and different diseases. As such there is a need for the preservation and the characterization of the banana cultivar population for the purposes of crop improvement. The identification of collected banana germplasm in Zimbabwe was conducted based on the Inter-transcribed spacer region as well as morphology. The study was conducted with the aim of distinguishing one cultivar from another towards genetic conservation as well as banana improvement. RESULTS ITS 1 and ITS 4 region targeting primers were used to amplify the DNA from twelve cultivars as well as sequence. Blast results identified five Musa groups which are Musa balbisiana (BB), Musa ABB, Musa AB hybrid, Musa acuminata (AAA), and Musa acuminata subsp. Malaccensis (AA). Phylogenetic analysis was done on the sequences under study and a maximum likelihood tree was generated to determine relationships between the sequences. Further identification was done using the inflorescence, bract, and male bud and fruit characteristics of each cultivar complementing the molecular evaluation. CONCLUSION Genetic and morphological identification of locally grown bananas was therefore successful. An important step towards identifying pure lines suitable for breeding.
Collapse
Affiliation(s)
- Kumbirai Beaton
- Department of Biotechnology, Chinhoyi University of Technology, P.Bag 7724, Chinhoyi, Zimbabwe.
| | - Allen Mazadza
- Department of Biotechnology, Chinhoyi University of Technology, P.Bag 7724, Chinhoyi, Zimbabwe
| | - Zedias Chikwambi
- Department of Biotechnology, Chinhoyi University of Technology, P.Bag 7724, Chinhoyi, Zimbabwe
| |
Collapse
|
3
|
Kimutai C, Ndlovu N, Chaikam V, Ertiro BT, Das B, Beyene Y, Kiplagat O, Spillane C, Prasanna BM, Gowda M. Discovery of genomic regions associated with grain yield and agronomic traits in Bi-parental populations of maize ( Zea mays. L) Under optimum and low nitrogen conditions. Front Genet 2023; 14:1266402. [PMID: 37964777 PMCID: PMC10641019 DOI: 10.3389/fgene.2023.1266402] [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: 07/24/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023] Open
Abstract
Low soil nitrogen levels, compounded by the high costs associated with nitrogen supplementation through fertilizers, significantly contribute to food insecurity, malnutrition, and rural poverty in maize-dependent smallholder communities of sub-Saharan Africa (SSA). The discovery of genomic regions associated with low nitrogen tolerance in maize can enhance selection efficiency and facilitate the development of improved varieties. To elucidate the genetic architecture of grain yield (GY) and its associated traits (anthesis-silking interval (ASI), anthesis date (AD), plant height (PH), ear position (EPO), and ear height (EH)) under different soil nitrogen regimes, four F3 maize populations were evaluated in Kenya and Zimbabwe. GY and all the traits evaluated showed significant genotypic variance and moderate heritability under both optimum and low nitrogen stress conditions. A total of 91 quantitative trait loci (QTL) related to GY (11) and other secondary traits (AD (26), PH (19), EH (24), EPO (7) and ASI (4)) were detected. Under low soil nitrogen conditions, PH and ASI had the highest number of QTLs. Furthermore, some common QTLs were identified between secondary traits under both nitrogen regimes. These QTLs are of significant value for further validation and possible rapid introgression into maize populations using marker-assisted selection. Identification of many QTL with minor effects indicates genomic selection (GS) is more appropriate for their improvement. Genomic prediction within each population revealed low to moderately high accuracy under optimum and low soil N stress management. However, the accuracies were higher for GY, PH and EH under optimum compared to low soil N stress. Our findings indicate that genetic gain can be improved in maize breeding for low N stress tolerance by using GS.
Collapse
Affiliation(s)
- Collins Kimutai
- Seed, Crop and Horticultural Sciences, School of Agriculture and Biotechnology, University of Eldoret, Eldoret, Kenya
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Noel Ndlovu
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway, Ireland
| | - Vijay Chaikam
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | | | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Oliver Kiplagat
- Seed, Crop and Horticultural Sciences, School of Agriculture and Biotechnology, University of Eldoret, Eldoret, Kenya
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, Galway, Ireland
| | | | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| |
Collapse
|
4
|
Sedah P, Djedatin LG, Loko LYE, Ewedje EEBK, Orobiyi A, Gbemavo CDSJ, Toffa J, Tchakpa C, Cubry P, Sabot F. Impact of Seed Origin and Genetic Drift of Improved Rice Variety IR841 in Benin. RICE (NEW YORK, N.Y.) 2023; 16:48. [PMID: 37878087 PMCID: PMC10600083 DOI: 10.1186/s12284-023-00657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 08/26/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Rice production is important for food security in Benin, with a national production largely dominated by the cultivation of the aromatic ecotype IR841, by far the most appreciated by Beninese consumers. However, to maintain agronomical qualities of a given cultivar, the origin and quality of seeds are mandatory and at the heart of the maintenance of yield and of market requests. Following this idea, the objective of the current study was thus to investigate the genetic purity of IR841 varieties collected from rice producers across 22 villages in Benin in relation to their agronomical performances. RESULTS For this, agromorphological evaluation of 72 accessions based on 13 quantitative descriptors followed by genotyping with the Illumina Infinium rice 7 K SNP array of 9 accessions was carried out in the presence of 2 controls. Agromorphologic as well as genetic and phylogenetic analyses revealed two groups, the first one Okouta97, Koum47, Nana30, Man118, Ang1 and control sample IR841-2) was characterized by seed accessions provided by the formal seed system, while the second (Koum53, Tchaka41 and Koud46) comprising seeds from local markets or from previous harvests and showing a depression in agronomic performances. CONCLUSION We showed that IR841 seed purity is mandatory for the completion of agronomical performance, and that the farmers' choice of seeds must be guided and informed to ensure sustainability and food security.
Collapse
Affiliation(s)
- Paulin Sedah
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Lambert Gustave Djedatin
- Ecole Normale Supérieure de l'Enseignement Technique (ENSET), Lokossa, Bénin.
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin.
| | - Laura Yêyinou Estelle Loko
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Eben-Ezer Baba Kayodé Ewedje
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Azize Orobiyi
- Centre de Recherche Agricole Plantes Pérennes (CRA-PP- INRAB), Pobè, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Chalemagne Dossou Seblodo Judes Gbemavo
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Joelle Toffa
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Cyrille Tchakpa
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Philippe Cubry
- DIADE unit, UM, CIRAD IRD, Centre IRD de Montpellier, 911 Agropolis BP 604501, Montpellier Cedex 5, F- 34 394, France
| | - Francois Sabot
- DIADE unit, UM, CIRAD IRD, Centre IRD de Montpellier, 911 Agropolis BP 604501, Montpellier Cedex 5, F- 34 394, France
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| |
Collapse
|
5
|
Dossa EN, Shimelis H, Mrema E, Shayanowako ATI, Laing M. Genetic resources and breeding of maize for Striga resistance: a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1163785. [PMID: 37235028 PMCID: PMC10206272 DOI: 10.3389/fpls.2023.1163785] [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: 02/11/2023] [Accepted: 04/07/2023] [Indexed: 05/28/2023]
Abstract
The potential yield of maize (Zea mays L.) and other major crops is curtailed by several biotic, abiotic, and socio-economic constraints. Parasitic weeds, Striga spp., are major constraints to cereal and legume crop production in sub-Saharan Africa (SSA). Yield losses reaching 100% are reported in maize under severe Striga infestation. Breeding for Striga resistance has been shown to be the most economical, feasible, and sustainable approach for resource-poor farmers and for being environmentally friendly. Knowledge of the genetic and genomic resources and components of Striga resistance is vital to guide genetic analysis and precision breeding of maize varieties with desirable product profiles under Striga infestation. This review aims to present the genetic and genomic resources, research progress, and opportunities in the genetic analysis of Striga resistance and yield components in maize for breeding. The paper outlines the vital genetic resources of maize for Striga resistance, including landraces, wild relatives, mutants, and synthetic varieties, followed by breeding technologies and genomic resources. Integrating conventional breeding, mutation breeding, and genomic-assisted breeding [i.e., marker-assisted selection, quantitative trait loci (QTL) analysis, next-generation sequencing, and genome editing] will enhance genetic gains in Striga resistance breeding programs. This review may guide new variety designs for Striga-resistance and desirable product profiles in maize.
Collapse
Affiliation(s)
- Emeline Nanou Dossa
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Emmanuel Mrema
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Tanzania Agricultural Research Institute, Tumbi Center, Tabora, Tanzania
| | | | - Mark Laing
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| |
Collapse
|
6
|
Ayesiga SB, Rubaihayo P, Oloka BM, Dramadri IO, Edema R, Sserumaga JP. Genetic Variation Among Tropical Maize Inbred Lines from NARS and CGIAR Breeding Programs. PLANT MOLECULAR BIOLOGY REPORTER 2023; 41:209-217. [PMID: 37159650 PMCID: PMC10160135 DOI: 10.1007/s11105-022-01358-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/02/2022] [Indexed: 05/11/2023]
Abstract
The use of molecular markers allows for precise estimates of genetic diversity, which is an important parameter that enables breeders to select parental lines and designing breeding systems. We assessed the level of genetic diversity and population structure in a panel of 151 tropical maize inbred lines using 10,940 SNP (single nucleotide polymorphism) markers generated through the DArTseq genotyping platform. The average gene diversity was 0.39 with expected heterozygosity ranging from 0.00 to 0.84, and a mean of 0.02. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual inbred lines within the populations while only 3% was distributed among the populations. Both neighbor-joining clustering and STRUCTURE analysis classified the inbred lines into four major groups. The crosses that involve inbred lines from most divergent subgroups are expected to generate maximum heterosis and produce wide variation. The results will be beneficial for breeders to better understand and exploit the genetic diversity available in the set of maize inbred lines we studied. Supplementary Information The online version contains supplementary material available at 10.1007/s11105-022-01358-2.
Collapse
Affiliation(s)
- Stella Bigirwa Ayesiga
- Department of Agricultural Production, College of Agriculture and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
- Makerere University Regional Center for Crop Improvement (MaRCCI), College of Agriculture and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Patrick Rubaihayo
- Department of Agricultural Production, College of Agriculture and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Bonny Michael Oloka
- National Crops Resources Research Institute, National Agricultural Research Organization, P.O. Box 7084, Kampala, Uganda
| | - Isaac Onziga Dramadri
- Department of Agricultural Production, College of Agriculture and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
- Makerere University Regional Center for Crop Improvement (MaRCCI), College of Agriculture and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Richard Edema
- Department of Agricultural Production, College of Agriculture and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
- Makerere University Regional Center for Crop Improvement (MaRCCI), College of Agriculture and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Julius Pyton Sserumaga
- National Livestock Resources Research Institute, National Agricultural Research Organization, P.O. Box 5704, Kampala, Uganda
| |
Collapse
|
7
|
Adu GB, Badu-Apraku B, Akromah R, Awuku FJ. Combining Abilities and Heterotic Patterns among Early Maturing Maize Inbred Lines under Optimal and Striga-Infested Environments. Genes (Basel) 2022; 13:genes13122289. [PMID: 36553556 PMCID: PMC9778638 DOI: 10.3390/genes13122289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
Information on the general combining ability of inbred lines and the specific combining ability of hybrid combinations is crucial for successful hybrid development. The objectives of this study were to (i) determine the combining ability of thirty selected early maturing maize inbred lines under Striga-infested and optimal environments, (ii) classify the inbred lines into heterotic groups using the general combining ability effects of multiple traits (HGCAMT) and the single nucleotide polymorphism genetic distance (SNP- GD) methods, and (iii) assess the effectiveness of the heterotic grouping methods. One hundred and fifty single-cross hybrids were generated from the thirty inbred lines using the North Carolina Design II mating method. The hybrids and six local check varieties were tested across optimal and Striga-infested environments in Ghana and Nigeria in 2016 and 2017. The inheritance of grain yield was controlled by the non-additive gene action under both environments and the additive gene action across the two research environments. The non-additive gene action modulated the inheritance of measured traits under Striga-infested environments, except for the Striga damage syndrome rating at 8 weeks after planting. Maternal effects were observed for most traits in each environment and across environments. The inbred lines TZEI 127 and TZEI 40 exhibited significant and positive GCA male and female effects for grain yield under each environment and across the two research environments, indicating the presence of favorable alleles for yield improvements. The SNP-GD heterotic grouping method was identified as the most adequate in grouping the thirty inbred lines.
Collapse
Affiliation(s)
- Gloria Boakyewaa Adu
- Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute (SARI), Tamale, Ghana
- Correspondence: (G.B.A.); (B.B.-A.)
| | - Baffour Badu-Apraku
- International Institute of Tropical Agriculture (UK) Limited, Carolyn House, 26 Dingwall Road, Croydon CR0 9XP, UK
- Correspondence: (G.B.A.); (B.B.-A.)
| | - Richard Akromah
- Department of Crop and Soil Sciences, Faculty of Agriculture, Kwame Nkrumah University of Science and Technology, Private Mail Bag, University Post Office, Kumasi, Ghana
| | - Frederick Justice Awuku
- Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute (SARI), Tamale, Ghana
| |
Collapse
|
8
|
Maazou ARS, Gedil M, Adetimirin VO, Mengesha W, Meseka S, Ilesanmi O, Agre PA, Menkir A. Optimizing use of U.S. Ex-PVP inbred lines for enhancing agronomic performance of tropical Striga resistant maize inbred lines. BMC PLANT BIOLOGY 2022; 22:286. [PMID: 35681124 PMCID: PMC9185936 DOI: 10.1186/s12870-022-03662-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Temperate maize inbred lines with expired Plant Variety Protection Act certificates (Ex-PVP) are potential sources of desirable alleles for tropical germplasm improvement. Up to now, the usefulness of the Ex-PVP inbred lines as a potential source of novel beneficial alleles for Striga hermonthica resistance breeding to enhance genetic gain in tropical maize has not been reported. RESULTS This study was thus conducted to characterize the combining ability of 24 Ex-PVP inbred lines in crosses with two tropical Striga resistant inbred testers under Striga-infested and non-infested conditions and across three locations for 2 years. Many testcrosses between Ex-PVP inbred lines and the first tester (T1) produced competitive or significantly higher grain yields compared to the hybrid between the two resistant testers under Striga infested and non-infested conditions and across multiple test locations. Also, most of the testcrosses with positive heterosis for grain yield and negative heterosis for Striga damage and emerged Striga count involved T1 as a tester. Our study identified six Ex-PVP inbred lines with positive GCA effects for grain yield under Striga infested and non-infested conditions and across multiple test locations. Amongst these, inbred lines HB8229-1 and WIL900-1 also displayed negative GCA effects for emerged Striga count and Striga damage rating. The inbred line HB8229-1 showed positive SCA effects for grain yield with T2, whereas WIL900-1 had positive SCA effects for grain yield with T1. Over 70% of the Ex-PVP inbred lines were consistently assigned to specific heterotic groups using yield-based classifying methods (mean grain yield and SCA effects). CONCLUSIONS These results could facilitate systematic introgression of the Ex-PVP inbred lines into the existing Striga resistant heterotic groups in IITA. The Ex-PVP inbred lines with positive GCA effects and producing high grain yields in hybrid combinations could be useful parents for enhancing Striga resistance and agronomic performance of tropical maize hybrids.
Collapse
Affiliation(s)
- Abdoul-Raouf Sayadi Maazou
- Pan African University Life and Earth Sciences Institute (Including Health and Agriculture), University of Ibadan, Ibadan, 200284, Nigeria
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, 200001, Nigeria
| | - Melaku Gedil
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, 200001, Nigeria
| | - Victor O Adetimirin
- Department of Crop and Horticultural Sciences, University of Ibadan, Ibadan, 200284, Nigeria
| | - Wende Mengesha
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, 200001, Nigeria
| | - Silvestro Meseka
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, 200001, Nigeria
| | - Oluyinka Ilesanmi
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, 200001, Nigeria
| | - Paterne A Agre
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, 200001, Nigeria
| | - Abebe Menkir
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, 200001, Nigeria.
| |
Collapse
|
9
|
Population Structure Analysis and Association Mapping for Turcicum Leaf Blight Resistance in Tropical Maize Using SSR Markers. Genes (Basel) 2022; 13:genes13040618. [PMID: 35456424 PMCID: PMC9030036 DOI: 10.3390/genes13040618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 12/04/2022] Open
Abstract
Maize is an important cereal crop in the world for feed, food, fodder, and raw materials of industries. Turcicum leaf blight (TLB) is a major foliar disease that can cause more than 50% yield losses in maize. Considering this, the molecular diversity, population structure, and genome-wide association study (GWAS) for TLB resistance were studied in 288 diverse inbred lines genotyped using 89 polymorphic simple sequence repeats (SSR) markers. These lines werescreened for TLB disease at two hot-spot locations under artificially inoculated conditions. The average percent disease incidence (PDI) calculated for each genotype ranged from 17 (UMI 1201) to 78% (IML 12-22) with an overall mean of 40%. The numbers of alleles detected at a locus ranged from twoto nine, with a total of 388 alleles. The polymorphic information content (PIC) of each marker ranged between 0.04 and 0.86. Out of 89 markers, 47 markers were highly polymorphic (PIC ≥ 0.60). This indicated that the SSR markers used were very informative and suitable for genetic diversity, population structure, and marker-trait association studies.The overall observed homozygosity for highly polymorphic markers was 0.98, which indicated that lines used were genetically pure. Neighbor-joining clustering, factorial analysis, and population structure studies clustered the 288 lines into 3–5 groups. The patterns of grouping were in agreement with the origin and pedigree records of the genotypesto a greater extent.A total of 94.10% lines were successfully assigned to one or another group at a membership probability of ≥0.60. An analysis of molecular variance (AMOVA) revealed highly significant differences among populations and within individuals. Linkage disequilibrium for r2 and D′ between loci ranged from 0 to 0.77 and 0 to 1, respectively. A marker trait association analysis carried out using a general linear model (GLM) and mixed linear model (MLM), identified 15 SSRs markers significantly associated with TLB resistance.These 15 markers were located on almost all chromosomes (Chr) except 7, 8, and 9. The phenotypic variation explained by these loci ranged from 6% (umc1367) to 26% (nc130, phi085). Maximum 7 associated markers were located together on Chr 2 and 5. The selected regions identified on Chr 2 and 5 corroborated the previous studies carried out in the Indian maize germplasm. Further, 11 candidate genes were identified to be associated with significant markers. The identified sources for TLB resistance and associated markers may be utilized in molecular breeding for the development of suitable genotypes.
Collapse
|
10
|
Amegbor I, van Biljon A, Shargie N, Tarekegne A, Labuschagne M. Identifying Quality Protein Maize Inbred Lines for Improved Nutritional Value of Maize in Southern Africa. Foods 2022; 11:foods11070898. [PMID: 35406985 PMCID: PMC8998117 DOI: 10.3390/foods11070898] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 12/10/2022] Open
Abstract
Malnutrition, as a result of deficiency in essential nutrients in cereal food products and consumption of a poorly balanced diet, is a major challenge facing millions of people in developing countries. However, developing maize inbred lines that are high yielding with enhanced nutritional traits for hybrid development remains a challenge. This study evaluated 40 inbred lines: 26 quality protein maize (QPM) lines, nine non-QPM lines, and five checks (three QPM lines and two non-QPM lines) in four optimum environments in Zimbabwe and South Africa. The objective of the study was to identify good-quality QPM inbred lines for future hybrid breeding efforts in order to increase the nutritional value of maize. The QPM lines had a lower protein content (7% lower) than that of the non-QPM lines but had 1.9 times more tryptophan and double the quality index. The lysine- and tryptophan-poor α-zein protein fraction was 41% lower in QPM than in non-QPM, with a subsequent increase in γ-zein. There was significant variation within the QPM inbred lines for all measured quality characteristics, indicating that the best lines can be selected from this material without a yield penalty. QPM lines that had both high protein and tryptophan levels, which can be used as parents for highly nutritious hybrids, were identified.
Collapse
Affiliation(s)
- Isaac Amegbor
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa; (I.A.); (A.v.B.)
- CSIR—Savanna Agricultural Research Institute, Tamale 00233, Ghana
| | - Angeline van Biljon
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa; (I.A.); (A.v.B.)
| | - Nemera Shargie
- Agricultural Research Council—Grain Crops, Potchefstroom 2520, South Africa;
| | | | - Maryke Labuschagne
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa; (I.A.); (A.v.B.)
- Correspondence: ; Tel.: +27-51-4012-715
| |
Collapse
|
11
|
Osuman AS, Badu-Apraku B, Karikari B, Ifie BE, Tongoona P, Danquah EY. Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm. Genes (Basel) 2022; 13:genes13020349. [PMID: 35205393 PMCID: PMC8871853 DOI: 10.3390/genes13020349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 11/19/2022] Open
Abstract
Maize (Zea mays L.) production is constrained by drought and heat stresses. The combination of these two stresses is likely to be more detrimental. To breed for maize cultivars tolerant of these stresses, 162 tropical maize inbred lines were evaluated under combined heat and drought (CHD) and terminal drought (TD) conditions. The mixed linear model was employed for the genome-wide association study using 7834 SNP markers and several phenotypic data including, days to 50% anthesis (AD) and silking (SD), husk cover (HUSKC), and grain yield (GY). In total, 66, 27, and 24 SNPs were associated with the traits evaluated under CHD, TD, and their combined effects, respectively. Of these, four single nucleotide polymorphism (SNP) markers (SNP_161703060 on Chr01, SNP_196800695 on Chr02, SNP_195454836 on Chr05, and SNP_51772182 on Chr07) had pleiotropic effects on both AD and SD under CHD conditions. Four SNPs (SNP_138825271 (Chr03), SNP_244895453 (Chr04), SNP_168561609 (Chr05), and SNP_62970998 (Chr06)) were associated with AD, SD, and HUSKC under TD. Twelve candidate genes containing phytohormone cis-acting regulating elements were implicated in the regulation of plant responses to multiple stress conditions including heat and drought. The SNPs and candidate genes identified in the study will provide invaluable information for breeding climate smart maize varieties under tropical conditions following validation of the SNP markers.
Collapse
Affiliation(s)
- Alimatu Sadia Osuman
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra 00223, Ghana; (A.S.O.); (B.E.I.); (P.T.); (E.Y.D.)
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, Nigeria
- Crops Research Institute, P.O. Box 3785, Kumasi 00223, Ghana
| | - Baffour Badu-Apraku
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan 200001, Nigeria
- Correspondence: ; Tel.: +234-810-848-2590
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, P.O. Box TL 1882, Tamale 00223, Ghana;
| | - Beatrice Elohor Ifie
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra 00223, Ghana; (A.S.O.); (B.E.I.); (P.T.); (E.Y.D.)
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra 00223, Ghana; (A.S.O.); (B.E.I.); (P.T.); (E.Y.D.)
| | - Eric Yirenkyi Danquah
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, PMB 30 Legon, Accra 00223, Ghana; (A.S.O.); (B.E.I.); (P.T.); (E.Y.D.)
| |
Collapse
|
12
|
de Faria SV, Zuffo LT, Rezende WM, Caixeta DG, Pereira HD, Azevedo CF, DeLima RO. Phenotypic and molecular characterization of a set of tropical maize inbred lines from a public breeding program in Brazil. BMC Genomics 2022; 23:54. [PMID: 35030994 PMCID: PMC8759194 DOI: 10.1186/s12864-021-08127-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022] Open
Abstract
Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08127-7.
Collapse
Affiliation(s)
| | - Leandro Tonello Zuffo
- Department of Agronomy, Universidade Federal de Viçosa, Minas Gerais, Viçosa, Brazil
| | | | | | | | | | | |
Collapse
|
13
|
Malle S. Population Structure and Relatedness for Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:185-196. [PMID: 35641766 DOI: 10.1007/978-1-0716-2237-7_12] [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] [Indexed: 06/15/2023]
Abstract
The estimation of the population structure and genetic relatedness between individuals within a collection of accessions is important in the formation of core collections for the conservation of genetic resources, uncovering the demographic history of the population under study, as well as for association studies. With the recent development of high-throughput genotyping technologies, several algorithms and methods have been developed and implemented in software to estimate the extent of genetic diversity between individuals. In this chapter, our objective is to describe methods to capture population structure and relatedness in a step-by-step fashion. To exemplify the process, two pruned datasets (14K and 243K SNP markers) were used to investigate population structure and relatedness among a soybean GWAS panel using different approaches and methods.
Collapse
Affiliation(s)
- Sidiki Malle
- Assistant professor at Institut Polytechnique Rural de Formation et de Recherche Appliquée (IPR/IFRA) de Katibougou, Koulikoro, Mali.
| |
Collapse
|
14
|
Semagn K, Iqbal M, Alachiotis N, N'Diaye A, Pozniak C, Spaner D. Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array. Sci Rep 2021; 11:23773. [PMID: 34893626 PMCID: PMC8664822 DOI: 10.1038/s41598-021-02666-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022] Open
Abstract
Previous molecular characterization studies conducted in Canadian wheat cultivars shed some light on the impact of plant breeding on genetic diversity, but the number of varieties and markers used was small. Here, we used 28,798 markers of the wheat 90K single nucleotide polymorphisms to (a) assess the extent of genetic diversity, relationship, population structure, and divergence among 174 historical and modern Canadian spring wheat varieties registered from 1905 to 2018 and 22 unregistered lines (hereinafter referred to as cultivars), and (b) identify genomic regions that had undergone selection. About 91% of the pairs of cultivars differed by 20-40% of the scored alleles, but only 7% of the pairs had kinship coefficients of < 0.250, suggesting the presence of a high proportion of redundancy in allelic composition. Although the 196 cultivars represented eight wheat classes, our results from phylogenetic, principal component, and the model-based population structure analyses revealed three groups, with no clear structure among most wheat classes, breeding programs, and breeding periods. FST statistics computed among different categorical variables showed little genetic differentiation (< 0.05) among breeding periods and breeding programs, but a diverse level of genetic differentiation among wheat classes and predicted groups. Diversity indices were the highest and lowest among cultivars registered from 1970 to 1980 and from 2011 to 2018, respectively. Using two outlier detection methods, we identified from 524 to 2314 SNPs and 41 selective sweeps of which some are close to genes with known phenotype, including plant height, photoperiodism, vernalization, gluten strength, and disease resistance.
Collapse
Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - Muhammad Iqbal
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Nikolaos Alachiotis
- Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, 3230, Enschede, OV, The Netherlands
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| |
Collapse
|
15
|
Identifying suitable tester for evaluating Striga resistant lines using DArTseq markers and agronomic traits. PLoS One 2021; 16:e0253481. [PMID: 34143833 PMCID: PMC8213128 DOI: 10.1371/journal.pone.0253481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/05/2021] [Indexed: 12/01/2022] Open
Abstract
A desirable tester that elicits greater genetic difference in Striga resistance among test crosses in a breeding program has not been reported. Therefore, this study was conducted to characterize 30 Striga resistant yellow endosperm maize inbred lines and three testers with varying resistance levels to Striga using DArTseq SNP markers and agronomic traits to identify a suitable tester for resistance hybrid breeding. Marker-based and agronomic trait-based genetic distances were estimated for yellow endosperm maize inbred lines and testers with varying resistance levels to Striga. The Marker-based cluster analysis separated the Striga resistant lines and testers into two distinct groups. Although the susceptible tester (T3) was the most distantly related to the 30 Striga resistant inbred lines, it exhibited a narrower range in genetic distance estimates and poor agronomic performance under Striga infestation in crosses with the resistant lines. In contrast, the resistant tester (T2) showed a broader range in genetic distance estimates in pairs with the 30 resistant lines. Also, it formed many high yielding hybrids with desirable traits under parasite pressure. Furthermore, the most significant positive association between agronomic trait-based and marker-based distance estimates (r = 0.389, P = 0.01) was observed when T2 has paired with the Striga resistant maize inbred lines. It thus appears that T2 may be used as a suitable tester to determine the breeding value of lines in hybrid maize resistance breeding programs. T2 was the most suitable tester, with a tolerant tester (T1) as an alternative tester to characterize the combining ability of Striga resistant maize inbred lines. This result can also encourage other breeders to investigate testers relative discriminating ability with varying levels of resistance in hybrid breeding for resistance to diseases, pests, and other parasitic plants.
Collapse
|
16
|
Abu P, Badu-Apraku B, Ifie BE, Tongoona P, Melomey LD, Offei SK. Genetic diversity and inter-trait relationship of tropical extra-early maturing quality protein maize inbred lines under low soil nitrogen stress. PLoS One 2021; 16:e0252506. [PMID: 34115794 PMCID: PMC8195346 DOI: 10.1371/journal.pone.0252506] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/17/2021] [Indexed: 11/18/2022] Open
Abstract
Information on the genetic diversity, population structure, and trait associations of germplasm resources is crucial for predicting hybrid performance. The objective of this study was to dissect the genetic diversity and population structure of extra-early yellow and orange quality protein maize (QPM) inbred lines and identify secondary traits for indirect selection for enhanced grain yield under low-soil nitrogen (LN). One hundred and ten inbred lines were assessed under LN (30 kg ha -1) and assayed for tryptophan content. The lines were genotyped using 2500 single nucleotide polymorphism (SNP) markers. Majority (85.4%) of the inbred lines exhibited wide pairwise genetic distances between 0.4801 and 0.600. Genetic distances were wider between yellow and orange endosperm lines and predicted high heterosis in crosses between parents of different endosperm colors. The unweighted pair group method with arithmetic mean (UPGMA) and the admixture model-based population structure method both grouped the lines into five clusters. The clustering was based on endosperm color, pedigree, and selection history but not on LN tolerance or tryptophan content. Genotype by trait biplot analysis revealed association of grain yield with plant height and ear height. TZEEQI 394 and TZEEIORQ 73A had high expressivity for these traits. Indirect selection for high grain yield among the inbred lines could be achieved using plant and ear heights as selection criteria. The wide genetic variability observed in this study suggested that the inbred lines could be important sources of beneficial alleles for LN breeding programs in SSA.
Collapse
Affiliation(s)
- Pearl Abu
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Baffour Badu-Apraku
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- * E-mail:
| | - Beatrice E. Ifie
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Leander D. Melomey
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Samuel K. Offei
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| |
Collapse
|
17
|
Badu-Apraku B, Garcia-Oliveira AL, Petroli CD, Hearne S, Adewale SA, Gedil M. Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa. BMC PLANT BIOLOGY 2021; 21:96. [PMID: 33596835 PMCID: PMC7888073 DOI: 10.1186/s12870-021-02829-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 01/07/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Assessment and effective utilization of genetic diversity in breeding programs is crucial for sustainable genetic improvement and rapid adaptation to changing breeding objectives. During the past two decades, the commercialization of the early and extra-early maturing cultivars has contributed to rapid expansion of maize into different agro-ecologies of sub-Saharan Africa (SSA) where maize has become an important component of the agricultural economy and played a vital role in food and nutritional security. The present study aimed at understanding the population structure and genetic variability among 439 early and extra-early maize inbred lines developed from three narrow-based and twenty-seven broad-based populations by the International Iinstitute of Tropical Agriculture Maize Improvement Program (IITA-MIP). These inbreds were genotyped using 9642 DArTseq-based single nucleotide polymorphism (SNP) markers distributed uniformly throughout the maize genome. RESULTS About 40.8% SNP markers were found highly informative and exhibited polymorphic information content (PIC) greater than 0.25. The minor allele frequency and PIC ranged from 0.015 to 0.500 and 0.029 to 0.375, respectively. The STRUCTURE, neighbour-joining phylogenetic tree and principal coordinate analysis (PCoA) grouped the inbred lines into four major classes generally consistent with the selection history, ancestry and kernel colour of the inbreds but indicated a complex pattern of the genetic structure. The pattern of grouping of the lines based on the STRUCTURE analysis was in concordance with the results of the PCoA and suggested greater number of sub-populations (K = 10). Generally, the classification of the inbred lines into heterotic groups based on SNP markers was reasonably reliable and in agreement with defined heterotic groups of previously identified testers based on combining ability studies. CONCLUSIONS Complete understanding of potential heterotic groups would be difficult to portray by depending solely on molecular markers. Therefore, planned crosses involving representative testers from opposing heterotic groups would be required to refine the existing heterotic groups. It is anticipated that the present set of inbreds could contribute new beneficial alleles for population improvement, development of hybrids and lines with potential to strengthen future breeding programs. Results of this study would help breeders in formulating breeding strategies for genetic enhancement and sustainable maize production in SSA.
Collapse
Affiliation(s)
- Baffour Badu-Apraku
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
| | - Ana Luísa Garcia-Oliveira
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, 56237 Texcoco, Mexico
| | - César Daniel Petroli
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, 56237 Texcoco, Mexico
| | - Sarah Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, 56237 Texcoco, Mexico
| | - Samuel Adeyemi Adewale
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
| | - Melaku Gedil
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
| |
Collapse
|
18
|
Wang Y, Lv H, Xiang X, Yang A, Feng Q, Dai P, Li Y, Jiang X, Liu G, Zhang X. Construction of a SNP Fingerprinting Database and Population Genetic Analysis of Cigar Tobacco Germplasm Resources in China. FRONTIERS IN PLANT SCIENCE 2021; 12:618133. [PMID: 33719288 PMCID: PMC7943628 DOI: 10.3389/fpls.2021.618133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/22/2021] [Indexed: 05/12/2023]
Abstract
Cigar tobacco is an important economic crop that is widely grown around the world. In recent years, varietal identification has become a frequent problem in germplasm preservation collections, which causes considerable inconvenience and uncertainty in the cataloging and preservation of cigar germplasm resources, in the selection of parental lines for breeding, and in the promotion and use of high quality varieties. Therefore, the use of DNA fingerprints to achieve rapid and accurate identification of varieties can play an important role in germplasm identification and property rights disputes. In this study, we used genotyping-by-sequencing (GBS) on 113 cigar tobacco accessions to develop SNP markers. After filtering, 580,942 high-quality SNPs were obtained. We used the 580,942 SNPs to perform principal component analysis (PCA), population structure analysis, and neighbor joining (NJ) cluster analysis on the 113 cigar tobacco accessions. The results showed that the accessions were not completely classified based on their geographical origins, and the genetic backgrounds of these cigar resources are complex and diverse. We further selected from these high-quality SNPs to obtained 163 SNP sites, 133 of which were successfully converted into KASP markers. Finally, 47 core KASP markers and 24 candidate core markers were developed. Using the core markers, we performed variety identification and fingerprinting in 216 cigar germplasm accessions. The results of SNP fingerprinting, 2D barcoding, and genetic analysis of cigar tobacco germplasm in this study provide a scientific basis for screening and identifying high-quality cigar tobacco germplasm, mining important genes, and broadening the basis of cigar tobacco genetics and subsequent breeding work at the molecular level.
Collapse
Affiliation(s)
- Yanyan Wang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Hongkun Lv
- Haikou Cigar Research Institute, Hainan Provincial Tobacco Company of China National Tobacco Corporation, Haikou, China
| | - Xiaohua Xiang
- Haikou Cigar Research Institute, Hainan Provincial Tobacco Company of China National Tobacco Corporation, Haikou, China
| | - Aiguo Yang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Quanfu Feng
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Peigang Dai
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yuan Li
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xun Jiang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Guoxiang Liu
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- *Correspondence: Guoxiang Liu
| | - Xingwei Zhang
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Xingwei Zhang
| |
Collapse
|
19
|
Kibe M, Nair SK, Das B, Bright JM, Makumbi D, Kinyua J, Suresh LM, Beyene Y, Olsen MS, Prasanna BM, Gowda M. Genetic Dissection of Resistance to Gray Leaf Spot by Combining Genome-Wide Association, Linkage Mapping, and Genomic Prediction in Tropical Maize Germplasm. FRONTIERS IN PLANT SCIENCE 2020; 11:572027. [PMID: 33224163 PMCID: PMC7667048 DOI: 10.3389/fpls.2020.572027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/29/2020] [Indexed: 05/05/2023]
Abstract
Gray leaf spot (GLS) is one of the major maize foliar diseases in sub-Saharan Africa. Resistance to GLS is controlled by multiple genes with additive effect and is influenced by both genotype and environment. The objectives of the study were to dissect the genetic architecture of GLS resistance through linkage mapping and genome-wide association study (GWAS) and assessing the potential of genomic prediction (GP). We used both biparental populations and an association mapping panel of 410 diverse tropical/subtropical inbred lines that were genotyped using genotype by sequencing. Phenotypic evaluation in two to four environments revealed significant genotypic variation and moderate to high heritability estimates ranging from 0.43 to 0.69. GLS was negatively and significantly correlated with grain yield, anthesis date, and plant height. Linkage mapping in five populations revealed 22 quantitative trait loci (QTLs) for GLS resistance. A QTL on chromosome 7 (qGLS7-105) is a major-effect QTL that explained 28.2% of phenotypic variance. Together, all the detected QTLs explained 10.50, 49.70, 23.67, 18.05, and 28.71% of phenotypic variance in doubled haploid (DH) populations 1, 2, 3, and F3 populations 4 and 5, respectively. Joint linkage association mapping across three DH populations detected 14 QTLs that individually explained 0.10-15.7% of phenotypic variance. GWAS revealed 10 significantly (p < 9.5 × 10-6) associated SNPs distributed on chromosomes 1, 2, 6, 7, and 8, which individually explained 6-8% of phenotypic variance. A set of nine candidate genes co-located or in physical proximity to the significant SNPs with roles in plant defense against pathogens were identified. GP revealed low to moderate prediction correlations of 0.39, 0.37, 0.56, 0.30, 0.29, and 0.38 for within IMAS association panel, DH pop1, DH pop2, DH pop3, F3 pop4, and F3 po5, respectively, and accuracy was increased substantially to 0.84 for prediction across three DH populations. When the diversity panel was used as training set to predict the accuracy of GLS resistance in biparental population, there was 20-50% reduction compared to prediction within populations. Overall, the study revealed that resistance to GLS is quantitative in nature and is controlled by many loci with a few major and many minor effects. The SNPs/QTLs identified by GWAS and linkage mapping can be potential targets in improving GLS resistance in breeding programs, while GP further consolidates the development of high GLS-resistant lines by incorporating most of the major- and minor-effect genes.
Collapse
Affiliation(s)
- Maguta Kibe
- International Maize and Wheat Improvement Center, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Sudha K. Nair
- International Maize and Wheat Improvement Center, Hyderabad, India
| | - Biswanath Das
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Jumbo M. Bright
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Dan Makumbi
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Johnson Kinyua
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - L. M. Suresh
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Michael S. Olsen
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | | | - Manje Gowda
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| |
Collapse
|
20
|
Sserumaga JP, Makumbi D, Assanga SO, Mageto EK, Njeri SG, Jumbo BM, Bruce AY. Identification and diversity of tropical maize inbred lines with resistance to common rust ( Puccinia sorghi Schwein). CROP SCIENCE 2020; 60:2971-2989. [PMID: 33536660 PMCID: PMC7839556 DOI: 10.1002/csc2.20345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 09/14/2020] [Indexed: 05/20/2023]
Abstract
Common rust (CR) caused by Puccinia sorghi Schwein is one of the major foliar diseases of maize (Zea mays L.) in Eastern and Southern Africa. This study was conducted to (i) evaluate the response of elite tropical adapted maize inbred lines to Puccinia sorghi and identify resistant lines (ii) examine associations between CR disease parameters and agronomic traits, and (iii) assess the genetic diversity of the inbred lines. Fifty inbred lines were evaluated in field trials for three seasons (2017-2019) in Uganda under artificial inoculation. Disease severity was rated on a 1-9 scale at 21 (Rust 1), 28 (Rust 2), and 35 (Rust 3) days after inoculation. Area under disease progress curve (AUDPC) was calculated. The genetic diversity of the lines was assessed using 44,975 single nucleotide polymorphism markers. Combined ANOVA across seasons showed significant (P < .001) line mean squares for the three rust scores and AUDPC. Heritability was high for Rust 2 (0.90), Rust 3 (0.83), and AUDPC (0.93). Of the 50 lines, 12 were highly resistant to CR. Inbred lines CKL1522, CKL05010, and CKL05017 had significantly lower Rust 3 scores and AUDPC compared to the resistant check CML444 and are potential donors of CR resistance alleles. The genetic correlations between CR disease resistance parameters were positive and strong. A neighbor-joining (NJ) tree and STRUCTURE suggested the presence of three major groups among the lines, with lines highly resistant to CR spread across the three groups. The genetic diversity among the highly resistant lines can be exploited by recycling genetically distant lines to develop new multiple disease resistant inbred lines for hybrid development and deployment.
Collapse
Affiliation(s)
- Julius Pyton Sserumaga
- National Agricultural Research Organization (NARO)National Livestock Resources Research Institute (NaLIRRI)P.O. Box 5704KampalaUganda
| | - Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Silvano O. Assanga
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
- Bayer Crop Science1506 Hwy 69 Suite 100WacoNE68460USA
| | - Edna K. Mageto
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
- AgReliant Genetics LLC1249 South AvenueBooneIA50036USA
| | - Susan G. Njeri
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
- Crop Science DivisionBayer East Africa Ltd.P.O. Box 30321‐00100NairobiKenya
| | - Bright M. Jumbo
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Anani Y. Bruce
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| |
Collapse
|
21
|
Sant’Ana GC, Espolador FG, Granato ÍSC, Mendonça LF, Fritsche-Neto R, Borém A. Population structure analysis and identification of genomic regions under selection associated with low-nitrogen tolerance in tropical maize lines. PLoS One 2020; 15:e0239900. [PMID: 32991596 PMCID: PMC7523979 DOI: 10.1371/journal.pone.0239900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/15/2020] [Indexed: 11/18/2022] Open
Abstract
Increasing low nitrogen (N) tolerance in maize is an important goal for food security and agricultural sustainability. In order to analyze the population structure of tropical maize lines and identify genomic regions associated with low-N tolerance, a set of 64 inbred lines were evaluated under low-N and optimal-N conditions. The low-N Agronomic Efficiency index (LNAE) of each line was calculated. The maize lines were genotyped using 417,112 SNPs markers. The grouping based on the LNAE values classified the lines into two phenotypic groups, the first comprised by genotypes with high LNAE (named H_LNAE group), while the second one comprised genotypes with low LNAE (named L_LNAE group). The H_LNAE and L_LNAE groups had LNAE mean values of 3,304 and 1,644, respectively. The population structure analysis revealed a weak relationship between genetic and phenotypic diversity. Pairs of lines were identified, having at the same time high LNAE and high genetic distance from each other. A set of 29 SNPs markers exhibited a significant difference in allelic frequencies (Fst > 0.2) between H_LNAE and L_LNAE groups. The Pearson's correlation between LNAE and the favorable alleles in this set of SNPs was 0.69. These SNPs could be useful for marker-assisted selection for low-N tolerance in maize breeding programs. The results of this study could help maize breeders identify accessions to be used in the development of low-N tolerant cultivars.
Collapse
Affiliation(s)
| | - Fernando Garcia Espolador
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Leandro Freitas Mendonça
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Roberto Fritsche-Neto
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- * E-mail:
| | - Aluízio Borém
- Department of Agronomy, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| |
Collapse
|
22
|
Stanley A, Menkir A, Paterne A, Ifie B, Tongoona P, Unachukwu N, Meseka S, Mengesha W, Gedil M. Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1223. [PMID: 32957613 PMCID: PMC7570130 DOI: 10.3390/plants9091223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 11/17/2022]
Abstract
Striga hermonthica is a serious biotic stress limiting maize production in sub-Saharan Africa. The limited information on the patterns of genetic diversity among maize inbred lines derived from source germplasm with mixed genetic backgrounds limits the development of inbred lines, hybrids, and synthetics with durable resistance to S. hermonthica. This study was conducted to assess the level of genetic diversity in a panel of 150 diverse maize inbred lines using agronomic and molecular data and also to infer the population structure among the inbred lines. Ten Striga-resistance-related traits were used for the phenotypic characterization, and 16,735 high-quality single-nucleotide polymorphisms (SNPs), identified by genotyping-by-sequencing (GBS), were used for molecular diversity. The phenotypic and molecular hierarchical cluster analyses grouped the inbred lines into five clusters, respectively. However, the grouping patterns between the phenotypic and molecular hierarchical cluster analyses were inconsistent due to non-overlapping information between the phenotypic and molecular data. The correlation between the phenotypic and molecular diversity matrices was very low (0.001), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and molecular diversity analyses. The joint phenotypic and genotypic diversity matrices grouped the inbred lines into three groups based on their reaction patterns to S. hermonthica, and this was able to exploit a broad estimate of the actual diversity among the inbred lines. The joint analysis shows an invaluable insight for measuring genetic diversity in the evaluated materials. The result indicates that wide genetic variability exists among the inbred lines and that the joint diversity analysis can be utilized to reliably assign the inbred lines into heterotic groups and also to enhance the level of resistance to Striga in new maize varieties.
Collapse
Affiliation(s)
- Adekemi Stanley
- West Africa Centre for Crop Improvement University of Ghana, Legon PMB 30, Ghana; (A.S.); (B.I.); (P.T.)
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Abebe Menkir
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Agre Paterne
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Beatrice Ifie
- West Africa Centre for Crop Improvement University of Ghana, Legon PMB 30, Ghana; (A.S.); (B.I.); (P.T.)
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement University of Ghana, Legon PMB 30, Ghana; (A.S.); (B.I.); (P.T.)
| | - Nnanna Unachukwu
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Silvestro Meseka
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Wende Mengesha
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Melaku Gedil
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| |
Collapse
|
23
|
Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing. Sci Rep 2020; 10:13995. [PMID: 32814806 PMCID: PMC7438528 DOI: 10.1038/s41598-020-70842-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may be heterogeneous with larger than expected intra-accession genetic variation. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), cultivated and landraces (O. glaberrima, O. sativa), and improved varieties derived through interspecific hybridizations. A total of 1,527 DNA samples were genotyped with 46,818 polymorphic single nucleotide polymorphisms (SNPs) using DArTseq. Various statistical analyses were performed on eleven datasets corresponding to 5 plants per accession individually and in a bulk (two sets), 10 plants individually and in a bulk (two sets), all 15 plants individually (one set), and a randomly sampled individual repeated six times (six sets). Overall, we arrived at broadly similar conclusions across 11 datasets in terms of SNP polymorphism, heterozygosity/heterogeneity, diversity indices, concordance among genetic dissimilarity matrices, population structure, and genetic differentiation; there were, however, a few discrepancies between some pairs of datasets. Detailed results of each sampling method, the concordance in their outputs, and the technical and cost implications of each method were discussed.
Collapse
|
24
|
Obeng-Bio E, Badu-Apraku B, Ifie BE, Danquah A, Blay ET, Dadzie MA, Noudifoulè GT, Talabi AO. Genetic diversity among early provitamin A quality protein maize inbred lines and the performance of derived hybrids under contrasting nitrogen environments. BMC Genet 2020; 21:78. [PMID: 32682388 PMCID: PMC7368723 DOI: 10.1186/s12863-020-00887-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/12/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Information on population structure and genetic diversity of germplasm in a breeding programme is useful because it enhances judicious utilisation of genetic resources to achieve breeding objectives. Seventy early maturing provitamin A (PVA) quality protein maize (QPM) inbreds developed by the IITA- maize improvement programme were genotyped using 8171 DArTseq markers. Furthermore, 96 hybrids derived from 24 selected inbreds plus four checks were evaluated under low-N and optimal environments in Nigeria during 2016 and 2017. Genotypic and phenotypic data of inbreds and hybrids respectively, were analysed to (i) assess the level of genetic dissimilarities and population structure of the inbreds, and (ii) investigate the grain yield performance of derived hybrids under low-N, optimal and across environments. RESULTS Genetic diversity among the seventy inbreds was high varying from 0.042 to 0.500 with an average of 0.357. Sixty-six inbred lines with probabilities ≥0.70 were assigned to a single group. The population structure analysis, the UPGMA phylogeny, and the principal Coordinate Analysis (PCoA) of the DArTseq markers revealed a clear separation of five groups and each followed pedigree records. Clustered inbreds displayed common characteristics including high PVA levels, and drought and low-N tolerance. The top performing hybrid, TZEIORQ 40 × TZEIORQ 26 out-yielded the best hybrid control, TZEIOR 127 × TZEIOR 57 by 8, 3, and 9% under low-N, optimal, and across environments, respectively. High repeatability estimates were detected for grain yield under each and across environments. Similarly, high breeding efficiency of 71, 70 and 72% were computed under low-N, optimal, and across environments, respectively. CONCLUSIONS The UPGMA clustering, the structure analysis, and the PCoA consistently revealed five groups which largely followed pedigree information indicating the existence of genetically distinct groups in the inbred lines. High repeatability and breeding efficiency values estimated for grain yield of hybrids under low-N, optimal and across environments demonstrated that high productive hybrids could be developed using inbreds from the opposing clusters identified by the DArTseq markers. The 15 top performing hybrids identified, particularly TZEIORQ 40 × TZEIORQ 26 and TZEIORQ 29 × TZEIORQ 43 should be further evaluated for release and commercialization in SSA.
Collapse
Affiliation(s)
| | - Baffour Badu-Apraku
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, Nigeria
| | - Beatrice Elohor Ifie
- West Africa Center for Crop Improvement (WACCI), University of Ghana, PBM 30 Legon, Accra, Ghana
| | - Agyemang Danquah
- West Africa Center for Crop Improvement (WACCI), University of Ghana, PBM 30 Legon, Accra, Ghana
| | - Essie Takyiwaa Blay
- West Africa Center for Crop Improvement (WACCI), University of Ghana, PBM 30 Legon, Accra, Ghana
| | | | | | - Abidemi Olutayo Talabi
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, Nigeria
| |
Collapse
|
25
|
Falk KG, Jubery TZ, O'Rourke JA, Singh A, Sarkar S, Ganapathysubramanian B, Singh AK. Soybean Root System Architecture Trait Study through Genotypic, Phenotypic, and Shape-Based Clusters. PLANT PHENOMICS (WASHINGTON, D.C.) 2020; 2020:1925495. [PMID: 33313543 PMCID: PMC7706349 DOI: 10.34133/2020/1925495] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 04/16/2020] [Indexed: 05/24/2023]
Abstract
We report a root system architecture (RSA) traits examination of a larger scale soybean accession set to study trait genetic diversity. Suffering from the limitation of scale, scope, and susceptibility to measurement variation, RSA traits are tedious to phenotype. Combining 35,448 SNPs with an imaging phenotyping platform, 292 accessions (replications = 14) were studied for RSA traits to decipher the genetic diversity. Based on literature search for root shape and morphology parameters, we used an ideotype-based approach to develop informative root (iRoot) categories using root traits. The RSA traits displayed genetic variability for root shape, length, number, mass, and angle. Soybean accessions clustered into eight genotype- and phenotype-based clusters and displayed similarity. Genotype-based clusters correlated with geographical origins. SNP profiles indicated that much of US origin genotypes lack genetic diversity for RSA traits, while diverse accession could infuse useful genetic variation for these traits. Shape-based clusters were created by integrating convolution neural net and Fourier transformation methods, enabling trait cataloging for breeding and research applications. The combination of genetic and phenotypic analyses in conjunction with machine learning and mathematical models provides opportunities for targeted root trait breeding efforts to maximize the beneficial genetic diversity for future genetic gains.
Collapse
Affiliation(s)
- Kevin G. Falk
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | | | - Jamie A. O'Rourke
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa, USA
| | | | | |
Collapse
|
26
|
Wegary D, Teklewold A, Prasanna BM, Ertiro BT, Alachiotis N, Negera D, Awas G, Abakemal D, Ogugo V, Gowda M, Semagn K. Molecular diversity and selective sweeps in maize inbred lines adapted to African highlands. Sci Rep 2019; 9:13490. [PMID: 31530852 PMCID: PMC6748982 DOI: 10.1038/s41598-019-49861-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/28/2019] [Indexed: 11/08/2022] Open
Abstract
Little is known on maize germplasm adapted to the African highland agro-ecologies. In this study, we analyzed high-density genotyping by sequencing (GBS) data of 298 African highland adapted maize inbred lines to (i) assess the extent of genetic purity, genetic relatedness, and population structure, and (ii) identify genomic regions that have undergone selection (selective sweeps) in response to adaptation to highland environments. Nearly 91% of the pairs of inbred lines differed by 30-36% of the scored alleles, but only 32% of the pairs of the inbred lines had relative kinship coefficient <0.050, which suggests the presence of substantial redundancy in allelic composition that may be due to repeated use of fewer genetic backgrounds (source germplasm) during line development. Results from different genetic relatedness and population structure analyses revealed three different groups, which generally agrees with pedigree information and breeding history, but less so by heterotic groups and endosperm modification. We identified 944 single nucleotide polymorphic (SNP) markers that fell within 22 selective sweeps that harbored 265 protein-coding candidate genes of which some of the candidate genes had known functions. Details of the candidate genes with known functions and differences in nucleotide diversity among groups predicted based on multivariate methods have been discussed.
Collapse
Affiliation(s)
- Dagne Wegary
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Adefris Teklewold
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia.
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya
| | - Berhanu T Ertiro
- Bako National Maize Research Center, Ethiopian Institute of Agricultural Research (EIAR), Addis Ababa, Ethiopia
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Demewez Negera
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Geremew Awas
- International Maize and Wheat Improvement Center (CIMMYT) - Ethiopia Office, ILRI Campus, CMC Road, Gurd Sholla, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Demissew Abakemal
- Ambo Agricultural Research Center, P.O. Box 37, West Shoa, Ambo, Ethiopia
| | - Veronica Ogugo
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya
| | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya
| | - Kassa Semagn
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, P.O. Box 1041-00621, Nairobi, Kenya.
- Africa Rice Center (AfricaRice), M'bé Research Station, 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
| |
Collapse
|
27
|
Boakyewaa Adu G, Badu-Apraku B, Akromah R, Garcia-Oliveira AL, Awuku FJ, Gedil M. Genetic diversity and population structure of early-maturing tropical maize inbred lines using SNP markers. PLoS One 2019; 14:e0214810. [PMID: 30964890 PMCID: PMC6456193 DOI: 10.1371/journal.pone.0214810] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/20/2019] [Indexed: 11/23/2022] Open
Abstract
Information on genetic diversity and population structure are very important in any breeding programme for the improvement of traits of interest and the development of outstanding products for commercialization. In the present study, we assessed the genetic diversity of 94 early-maturing white and yellow tropical maize inbred lines using single nucleotide polymorphism (SNP) markers. The larger number of SNP markers used in this study allowed a clearer inference of the population structure of the 94 inbred lines. Cluster analysis resolved the inbred lines into different clusters based on their pedigree, selection history and endosperm colour. However, three heterotic groups were revealed by population structure analysis, but additional field evaluation could be more informative to confirm the heterotic groups identified. Nevertheless, wide genetic variability existed among the inbred lines making them unique with the potential to contribute new beneficial alleles to maize breeding programmes in the tropics, especially in the West and Central Africa (WCA) sub-region.
Collapse
Affiliation(s)
| | - Baffour Badu-Apraku
- International Institute of Tropical Agriculture (UK) Limited, Carolyn House, Croydon, United Kignodm
- * E-mail:
| | - Richard Akromah
- Department of Crop and Soil Sciences, Faculty of Agriculture, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | - Melaku Gedil
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| |
Collapse
|
28
|
Sserumaga J, Makumbi D, Warburton M, Opiyo S, Asea G, Muwonge A, Kasozi C. Genetic Diversity among Tropical Provitamin A Maize Inbred Lines and Implications for a Biofortification Program. CEREAL RESEARCH COMMUNICATIONS 2019; 47:134-144. [PMID: 33304016 PMCID: PMC7680936 DOI: 10.1556/0806.46.2018.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/16/2018] [Indexed: 05/25/2023]
Abstract
Insights into the diversity and relationships among elite breeding materials are an important component in maize improvement programs. We genotyped 63 inbred lines bred for high levels of provitamin A using 137 single nucleotide polymorphism markers. A total of 272 alleles were detected with gene diversity of 0.36. Average genetic distance was 0.36 with 56% of the pairs of lines having between 0.30 and 0.40. Eighty-six percent of the pairs of lines showed relative kinship values <0.50, which indicated that the majority of these provitamin A inbred lines were unique. Relationship pattern and population structure analysis revealed presence of seven major groups with good agreement with Neighbour Joining clustering and somewhat correlated with pedigree and breeding origin. Utilization of this set of provitamin A lines in a new biofortification program will be aided by information from both molecular-based grouping and pedigree analysis. The results should guide breeders in selecting parents for hybrid formation and testing as a short-term objective, and parents with diverse alleles for new breeding starts as a long-term objective in a provitamin A breeding program.
Collapse
Affiliation(s)
- J.P. Sserumaga
- Cereals Program, National Agricultural Research Organization; National Crops Resources Research Institute, Namulonge, P. O. Box 7084 Kampala, Uganda
| | - D. Makumbi
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Nairobi, Kenya
| | - M.L. Warburton
- USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State, MS 39762
| | - S.O. Opiyo
- Molecular and Cellular Imaging Center, Ohio State University, Columbus, OH, 43210
| | - G. Asea
- Cereals Program, National Agricultural Research Organization; National Crops Resources Research Institute, Namulonge, P. O. Box 7084 Kampala, Uganda
| | - A. Muwonge
- Cereals Program, National Agricultural Research Organization; National Crops Resources Research Institute, Namulonge, P. O. Box 7084 Kampala, Uganda
| | - C.L. Kasozi
- Cereals Program, National Agricultural Research Organization; National Crops Resources Research Institute, Namulonge, P. O. Box 7084 Kampala, Uganda
| |
Collapse
|
29
|
|
30
|
Njeri SG, Makumbi D, Warburton ML, Diallo A, Jumbo MB, Chemining’wa G. Genetic analysis of tropical quality protein maize ( Zea mays L.) germplasm. EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2017; 213:261. [PMID: 33364631 PMCID: PMC7734200 DOI: 10.1007/s10681-017-2048-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 10/24/2017] [Indexed: 06/12/2023]
Abstract
Maize (Zea mays L.) is an important source of carbohydrates and protein in the diet in sub-Saharan Africa. The objectives of this study were to (i) estimate general (GCA) and specific combining abilities (SCA) of 13 new quality protein maize (QPM) lines in a diallel under stress and non-stress conditions, (ii) compare observed and predicted performance of QPM hybrids, (iii) characterize genetic diversity among the 13 QPM lines using single nucleotide polymorphism (SNP) markers and assess the relationship between genetic distance and hybrid performance, and (iv) assess diversity and population structure in 116 new QPM inbred lines as compared to eight older tropical QPM lines and 15 non-QPM lines. The GCA and SCA effects were significant for most traits under optimal conditions, indicating that both additive and non-additive genetic effects were important for inheritance of the traits. Additive genetic effects appeared to govern inheritance of most traits under optimal conditions and across environments. Non-additive genetic effects were more important for inheritance of grain yield but additive effects controlled most agronomic traits under drought stress conditions. Inbred lines CKL08056, CKL07292, and CKL07001 had desirable GCA effects for grain yield across drought stress and non-stress conditions. Prediction efficiency for grain yield was highest under optimal conditions. The classification of 139 inbred lines with 95 SNPs generated six clusters, four of which contained 10 or fewer lines, and 16 lines of mixed co-ancestry. There was good agreement between Neighbor Joining dendrogram and Structure classification. The QPM lines used in the diallel were nearly uniformly spread throughout the dendrogram. There was no relationship between genetic distance and grain yield in either the optimal or stressed environments in this study. The genetic diversity in mid-altitude maize germplasm is ample, and the addition of the QPM germplasm did not increase it measurably.
Collapse
Affiliation(s)
- Susan G. Njeri
- International Maize and Wheat Improvement Center (CIMMYT), P.O Box 1041-00621, Nairobi, Kenya
| | - Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT), P.O Box 1041-00621, Nairobi, Kenya
| | - Marilyn L. Warburton
- USDA ARS Corn Host Plant Resistance Research Unit, Box 9555, Mississippi State, MS 39762, USA
| | - Alpha Diallo
- International Maize and Wheat Improvement Center (CIMMYT), P.O Box 1041-00621, Nairobi, Kenya
- Guinee-Semences, Immeuble Guinomar, Camayenne, Corniche Nord, BP 5603, Conakry, Guinea
| | - MacDonald B. Jumbo
- International Maize and Wheat Improvement Center (CIMMYT), P.O Box 1041-00621, Nairobi, Kenya
| | - George Chemining’wa
- Department of Plant Science and Crop Protection, University of Nairobi, P.O. Box 29053-00625, Nairobi, Kenya
| |
Collapse
|
31
|
Ertiro BT, Semagn K, Das B, Olsen M, Labuschagne M, Worku M, Wegary D, Azmach G, Ogugo V, Keno T, Abebe B, Chibsa T, Menkir A. Genetic variation and population structure of maize inbred lines adapted to the mid-altitude sub-humid maize agro-ecology of Ethiopia using single nucleotide polymorphic (SNP) markers. BMC Genomics 2017; 18:777. [PMID: 29025420 PMCID: PMC5639748 DOI: 10.1186/s12864-017-4173-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 10/05/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular characterization is important for efficient utilization of germplasm and development of improved varieties. In the present study, we investigated the genetic purity, relatedness and population structure of 265 maize inbred lines from the Ethiopian Institute of Agricultural Research (EIAR), the International Maize and Wheat Improvement Centre (CIMMYT) and the International Institute of Tropical Agriculture (IITA) using 220,878 single nucleotide polymorphic (SNP) markers obtained using genotyping by sequencing (GBS). RESULTS Only 22% of the inbred lines were considered pure with <5% heterogeneity, while the remaining 78% of the inbred lines had a heterogeneity ranging from 5.1 to 31.5%. Pairwise genetic distances among the 265 inbred lines varied from 0.011 to 0.345, with 89% of the pairs falling between 0.301 and 0.345. Only <1% of the pairs had a genetic distance lower than 0.200, which included 14 pairs of sister lines that were nearly identical. Relative kinship analysis showed that the kinship coefficients for 59% of the pairs of lines was close to zero, which agrees with the genetic distance estimates. Principal coordinate analysis, discriminant analysis of principal components (DAPC) and the model-based population structure analysis consistently suggested the presence of three groups, which generally agreed with pedigree information (genetic background). Although not distinct enough, the SNP markers showed some level of separation between the two CIMMYT heterotic groups A and B established based on pedigree and combining ability information. CONCLUSIONS The high level of heterogeneity detected in most of the inbred lines suggested the requirement for purification or further inbreeding except those deliberately maintained at early inbreeding level. The genetic distance and relative kinship analysis clearly indicated the uniqueness of most of the inbred lines in the maize germplasm available for breeders in the mid-altitude maize breeding program of Ethiopia. Results from the present study facilitate the maize breeding work in Ethiopia and germplasm exchange among breeding programs in Africa. We suggest the incorporation of high density molecular marker information in future heterotic group assignments.
Collapse
Affiliation(s)
- Berhanu Tadesse Ertiro
- Bako National Maize Research Center, Ethiopian Institute of Agricultural Research (EIAR), Bako, West Shoa, Oromia, Ethiopia
| | - Kassa Semagn
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB T6G 2P5 Canada
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, Nairobi, 00621 Kenya
| | - Michael Olsen
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, Nairobi, 00621 Kenya
| | - Maryke Labuschagne
- Department of Plant Sciences, University of Free State, Bloemfontein, South Africa
| | - Mosisa Worku
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, Nairobi, 00621 Kenya
| | - Dagne Wegary
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 5689, Addis Ababa, Ethiopia
| | - Girum Azmach
- Bako National Maize Research Center, Ethiopian Institute of Agricultural Research (EIAR), Bako, West Shoa, Oromia, Ethiopia
| | - Veronica Ogugo
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, Nairobi, 00621 Kenya
| | - Tolera Keno
- Bako National Maize Research Center, Ethiopian Institute of Agricultural Research (EIAR), Bako, West Shoa, Oromia, Ethiopia
| | - Beyene Abebe
- Bako National Maize Research Center, Ethiopian Institute of Agricultural Research (EIAR), Bako, West Shoa, Oromia, Ethiopia
| | - Temesgen Chibsa
- Bako National Maize Research Center, Ethiopian Institute of Agricultural Research (EIAR), Bako, West Shoa, Oromia, Ethiopia
| | - Abebe Menkir
- International Institute of Tropical Agriculture, Oya road PMB, Ibadan, 5320 Nigeria
| |
Collapse
|
32
|
Ndjiondjop MN, Semagn K, Gouda AC, Kpeki SB, Dro Tia D, Sow M, Goungoulou A, Sie M, Perrier X, Ghesquiere A, Warburton ML. Genetic Variation and Population Structure of Oryza glaberrima and Development of a Mini-Core Collection Using DArTseq. FRONTIERS IN PLANT SCIENCE 2017; 8:1748. [PMID: 29093721 PMCID: PMC5651524 DOI: 10.3389/fpls.2017.01748] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/25/2017] [Indexed: 05/20/2023]
Abstract
The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97-99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1-89.2% attributable to differences within groups.
Collapse
Affiliation(s)
- Marie-Noelle Ndjiondjop
- Africa Rice Center (AfricaRice), Bouake, Cote d'Ivoire
- *Correspondence: Marie-Noelle Ndjiondjop
| | - Kassa Semagn
- Department of Agriculture, Forestry and Nutrition Science, University of Alberta, Edmonton, Canada
| | | | | | | | - Mounirou Sow
- Africa Rice Center (AfricaRice), Ibadan, Nigeria
| | | | - Moussa Sie
- Africa Rice Center (AfricaRice), Centre National de la Recherche Appliquée au Développement Rural (FOFIFA), Antananarivo, Madagascar
| | - Xavier Perrier
- Unité Mixte de Recherche Amélioration Génétique, CIRAD, Montpellier, France
- University of Montpellier, Montpellier, France
| | - Alain Ghesquiere
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Marilyn L. Warburton
- Corn Host Plant Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Starkville, Mississippi, United States
| |
Collapse
|
33
|
Chen J, Shrestha R, Ding J, Zheng H, Mu C, Wu J, Mahuku G. Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm. G3 (BETHESDA, MD.) 2016; 6:3803-3815. [PMID: 27742723 PMCID: PMC5144952 DOI: 10.1534/g3.116.034561] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/25/2016] [Indexed: 11/18/2022]
Abstract
Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1-4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four biparental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight colocated loci on chromosomes 2, 3, 4, 5, 9, and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize.
Collapse
Affiliation(s)
- Jiafa Chen
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
| | - Rosemary Shrestha
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
| | - Junqiang Ding
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongjian Zheng
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shangai 201403 China
| | - Chunhua Mu
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jianyu Wu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - George Mahuku
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
- International Institute of Tropical Agriculture, 34441 Dar es Salaam, Tanzania
| |
Collapse
|
34
|
de Andrade LRB, Fritsche Neto R, Granato ÍSC, Sant’Ana GC, Morais PPP, Borém A. Genetic Vulnerability and the Relationship of Commercial Germplasms of Maize in Brazil with the Nested Association Mapping Parents. PLoS One 2016; 11:e0163739. [PMID: 27780247 PMCID: PMC5079593 DOI: 10.1371/journal.pone.0163739] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/13/2016] [Indexed: 11/19/2022] Open
Abstract
A few breeding companies dominate the maize (Zea mays L.) hybrid market in Brazil: Monsanto® (35%), DuPont Pioneer® (30%), Dow Agrosciences® (15%), Syngenta® (10%) and Helix Sementes (4%). Therefore, it is important to monitor the genetic diversity in commercial germplasms as breeding practices, registration and marketing of new cultivars can lead to a significant reduction of the genetic diversity. Reduced genetic variation may lead to crop vulnerabilities, food insecurity and limited genetic gains following selection. The aim of this study was to evaluate the genetic vulnerability risk by examining the relationship between the commercial Brazilian maize germplasms and the Nested Association Mapping (NAM) Parents. For this purpose, we used the commercial hybrids with the largest market share in Brazil and the NAM parents. The hybrids were genotyped for 768 single nucleotide polymorphisms (SNPs), using the Illumina Goldengate® platform. The NAM parent genomic data, comprising 1,536 SNPs for each line, were obtained from the Panzea data bank. The population structure, genetic diversity and the correlation between allele frequencies were analyzed. Based on the estimated effective population size and genetic variability, it was found that there is a low risk of genetic vulnerability in the commercial Brazilian maize germplasms. However, the genetic diversity is lower than those found in the NAM parents. Furthermore, the Brazilian germplasms presented no close relations with most NAM parents, except B73. This indicates that B73, or its heterotic group (Iowa Stiff Stalk Synthetic), contributed to the development of the commercial Brazilian germplasms.
Collapse
Affiliation(s)
| | - Roberto Fritsche Neto
- Genetics Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- * E-mail:
| | | | - Gustavo César Sant’Ana
- Systèmes biologiques, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, Languedoc-Roussillo, France
| | | | - Aluízio Borém
- Plants Science Department, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| |
Collapse
|
35
|
Mahuku G, Chen J, Shrestha R, Narro LA, Guerrero KVO, Arcos AL, Xu Y. Combined linkage and association mapping identifies a major QTL (qRtsc8-1), conferring tar spot complex resistance in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1217-29. [PMID: 26971113 DOI: 10.1007/s00122-016-2698-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/18/2016] [Indexed: 05/22/2023]
Abstract
A major QTL ( qRtsc8 - 1 ) conditioning resistance to tar spot complex of maize and occurring at a frequency of 3.5 % across 890 maize inbred lines. Tar spot complex (TSC) is a highly destructive disease of maize found in some countries in America. Identification of TSC resistant germplasm and elucidating the genetic mechanism of resistance is crucial for the use of host resistance to manage this disease. We evaluated 890 elite maize inbred lines in multiple environments and used genome wide association analysis (GWAS) with genotypic data from Illumina MaizeSNP50 BeadChip containing 56 K SNPs to dissect the genetics of TSC resistance. GWAS results were validated through linkage analysis in three bi-parental populations derived from different resistant and susceptible parents. Through GWAS, three TSC resistance loci were identified on chromosome 2, 7 and 8 (-log10 (p) > 5.99). A major quantitative resistance locus (QTL) designated qRtsc8-1, was detected on maize chromosome bin 8.03. qRtsc8-1, was confirmed in three independent bi-parental populations and it accounted for 18-43 % of the observed phenotypic variation for TSC. A rare haplotype within the qRtsc8-1 region, occurring at a frequency of 3.5 % increased TSC resistance by 14 %. Candidate gene analysis revealed that a leucine-rich repeat receptor-like protein (LRR-RLKs) gene family maybe the candidate gene for qRtsc8-1. Identification and localization of a major locus conditioning TSC resistance provides the foundation for fine mapping qRtsc8-1 and developing functional markers for improving TSC resistance in maize breeding programs. To the best of our knowledge, this is the first report of a major QTL for TSC resistance.
Collapse
Affiliation(s)
- George Mahuku
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, PO Box 1041-00621, Nairobi, Kenya.
- International Institute of Tropical Agriculture (IITA), P.O.Box, 34443, Dar es Salaam, Tanzania.
| | - Jiafa Chen
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Rosemary Shrestha
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Luis A Narro
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Aereo 67-13, Cali, Colombia
| | | | - Alba Lucia Arcos
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Aereo 67-13, Cali, Colombia
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CIMMYT) and Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| |
Collapse
|
36
|
Wu Y, San Vicente F, Huang K, Dhliwayo T, Costich DE, Semagn K, Sudha N, Olsen M, Prasanna BM, Zhang X, Babu R. Molecular characterization of CIMMYT maize inbred lines with genotyping-by-sequencing SNPs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:753-765. [PMID: 26849239 PMCID: PMC4799255 DOI: 10.1007/s00122-016-2664-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 01/09/2016] [Indexed: 05/08/2023]
Abstract
Molecular characterization information on genetic diversity, population structure and genetic relationships provided by this research will help maize breeders to better understand how to utilize the current CML collection. CIMMYT maize inbred lines (CMLs) have been widely used all over the world and have contributed greatly to both tropical and temperate maize improvement. Genetic diversity and population structure of the current CML collection and of six temperate inbred lines were assessed and relationships among all lines were determined with genotyping-by-sequencing SNPs. Results indicated that: (1) wider genetic distance and low kinship coefficients among most pairs of lines reflected the uniqueness of most lines in the current CML collection; (2) the population structure and genetic divergence between the Temperate subgroup and Tropical subgroups were clear; three major environmental adaptation groups (Lowland Tropical, Subtropical/Mid-altitude and Highland Tropical subgroups) were clearly present in the current CML collection; (3) the genetic diversity of the three Tropical subgroups was similar and greater than that of the Temperate subgroup; the average genetic distance between the Temperate and Tropical subgroups was greater than among Tropical subgroups; and (4) heterotic patterns in each environmental adaptation group estimated using GBS SNPs were only partially consistent with patterns estimated based on combining ability tests and pedigree information. Combining current heterotic information based on combining ability tests and the genetic relationships inferred from molecular marker analyses may be the best strategy to define heterotic groups for future tropical maize improvement. Information resulting from this research will help breeders to better understand how to utilize all the CMLs to select parental lines, replace testers, assign heterotic groups and create a core set of breeding germplasm.
Collapse
Affiliation(s)
- Yongsheng Wu
- Maize Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, 530007, Guangxi, China
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Felix San Vicente
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Kaijian Huang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, 530007, Guangxi, China
| | - Thanda Dhliwayo
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Denise E Costich
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Kassa Semagn
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, Nairobi, 00621, Kenya
| | - Nair Sudha
- CIMMYT-India, C/O ICRISAT, Patancheru, 502324, Andhra Pradesh, India
| | - Michael Olsen
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, Nairobi, 00621, Kenya
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market, Nairobi, 00621, Kenya
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
| | - Raman Babu
- CIMMYT-India, C/O ICRISAT, Patancheru, 502324, Andhra Pradesh, India.
| |
Collapse
|
37
|
Wang K, Qiu F, Larazo W, Dela Paz MA, Xie F. Heterotic groups of tropical indica rice germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:421-30. [PMID: 25511903 DOI: 10.1007/s00122-014-2441-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 12/06/2014] [Indexed: 05/15/2023]
Abstract
Four heterotic groups were identified for tropical indica rice germplasm to develop hybrid rice in the tropics based on two studies. Heterotic groups are of fundamental importance in hybrid crop breeding. This study investigated hybrid yield, yield heterosis and combining ability within and among groups based on genetic distance derived from single-nucleotide polymorphism markers. The main objectives of the study were to (1) evaluate the magnitude of yield heterosis among marker-based groups, (2) identify possible heterotic groups for tropical indica hybrid rice, and (3) validate heterotic patterns concluded from a previous study. Seventeen rice parents selected from improved indica germplasm from the tropics with high genetic divergence and 136 derived hybrids were evaluated in five environments. The hybrids had more yield than their parents with an average of 24.1 % mid-parent heterosis. Genotype × environment interaction was the major factor affecting variations in yield and yield heterosis, which raised a necessity and a challenge to develop heterotic rice hybrid adapted to different regions and seasons in the tropics. Yield, yield heterosis and combining ability were significantly increased in inter-group than in intra-group hybrids. Four heterotic groups and three promising hybridization patterns, which could be used in tropical hybrid rice breeding, were identified based on marker-based grouping, yield and yield heterosis analyses in the two studies. The study reveals that molecular markers analysis can serve as a basis for assigning germplasm into heterotic groups and to provide guidelines for parental selection in hybrid rice breeding.
Collapse
Affiliation(s)
- Kai Wang
- International Rice Research Institute, DAPO Box 7777, 1301, Metro Manila, Philippines
| | | | | | | | | |
Collapse
|
38
|
Tian HL, Wang FG, Zhao JR, Yi HM, Wang L, Wang R, Yang Y, Song W. Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015. [PMID: 26052247 DOI: 10.1007/s11032-015-0202-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the maize (Zea mays L.) genome. SNPs have several advantages over simple sequence repeats, such as ease of data comparison and integration, high-throughput processing of loci, and identification of associated phenotypes. SNPs are thus ideal for DNA fingerprinting, genetic diversity analysis, and marker-assisted breeding. Here, we developed a high-throughput and compatible SNP array, maizeSNP3072, containing 3072 SNPs developed from the maizeSNP50 array. To improve genotyping efficiency, a high-quality cluster file, maizeSNP3072_GT.egt, was constructed. All 3072 SNP loci were localized within different genes, where they were distributed in exons (43 %), promoters (21 %), 3' untranslated regions (UTRs; 22 %), 5' UTRs (9 %), and introns (5 %). The average genotyping failure rate using these SNPs was only 6 %, or 3 % using the cluster file to call genotypes. The genotype consistency of repeat sample analysis on Illumina GoldenGate versus Infinium platforms exceeded 96.4 %. The minor allele frequency (MAF) of the SNPs averaged 0.37 based on data from 309 inbred lines. The 3072 SNPs were highly effective for distinguishing among 276 examined hybrids. Comparative analysis using Chinese varieties revealed that the 3072SNP array showed a better marker success rate and higher average MAF values, evaluation scores, and variety-distinguishing efficiency than the maizeSNP50K array. The maizeSNP3072 array thus can be successfully used in DNA fingerprinting identification of Chinese maize varieties and shows potential as a useful tool for germplasm resource evaluation and molecular marker-assisted breeding.
Collapse
Affiliation(s)
- Hong-Li Tian
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Feng-Ge Wang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Jiu-Ran Zhao
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Hong-Mei Yi
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Lu Wang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Rui Wang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Yang Yang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Wei Song
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| |
Collapse
|
39
|
Tian HL, Wang FG, Zhao JR, Yi HM, Wang L, Wang R, Yang Y, Song W. Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:136. [PMID: 26052247 PMCID: PMC4449932 DOI: 10.1007/s11032-015-0335-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 05/23/2015] [Indexed: 05/03/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the maize (Zea mays L.) genome. SNPs have several advantages over simple sequence repeats, such as ease of data comparison and integration, high-throughput processing of loci, and identification of associated phenotypes. SNPs are thus ideal for DNA fingerprinting, genetic diversity analysis, and marker-assisted breeding. Here, we developed a high-throughput and compatible SNP array, maizeSNP3072, containing 3072 SNPs developed from the maizeSNP50 array. To improve genotyping efficiency, a high-quality cluster file, maizeSNP3072_GT.egt, was constructed. All 3072 SNP loci were localized within different genes, where they were distributed in exons (43 %), promoters (21 %), 3' untranslated regions (UTRs; 22 %), 5' UTRs (9 %), and introns (5 %). The average genotyping failure rate using these SNPs was only 6 %, or 3 % using the cluster file to call genotypes. The genotype consistency of repeat sample analysis on Illumina GoldenGate versus Infinium platforms exceeded 96.4 %. The minor allele frequency (MAF) of the SNPs averaged 0.37 based on data from 309 inbred lines. The 3072 SNPs were highly effective for distinguishing among 276 examined hybrids. Comparative analysis using Chinese varieties revealed that the 3072SNP array showed a better marker success rate and higher average MAF values, evaluation scores, and variety-distinguishing efficiency than the maizeSNP50K array. The maizeSNP3072 array thus can be successfully used in DNA fingerprinting identification of Chinese maize varieties and shows potential as a useful tool for germplasm resource evaluation and molecular marker-assisted breeding.
Collapse
Affiliation(s)
- Hong-Li Tian
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Feng-Ge Wang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Jiu-Ran Zhao
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Hong-Mei Yi
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Lu Wang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Rui Wang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Yang Yang
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| | - Wei Song
- Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China
| |
Collapse
|
40
|
Manickavelu A, Jighly A, Ban T. Molecular evaluation of orphan Afghan common wheat (Triticum aestivum L.) landraces collected by Dr. Kihara using single nucleotide polymorphic markers. BMC PLANT BIOLOGY 2014; 14:320. [PMID: 25432399 PMCID: PMC4255927 DOI: 10.1186/s12870-014-0320-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 11/06/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Landraces are an important source of genetic diversity in common wheat, but archival collections of Afghan wheat landraces remain poorly characterised. The recent development of array based marker systems, particularly single nucleotide polymorphism (SNP) markers, provide an excellent tool for examining the genetic diversity of local populations. Here we used SNP analysis to demonstrate the importance of Afghan wheat landraces and found tremendous genetic diversity and province-specific characteristics unique to this geographic region. RESULTS A total of 446 Afghan wheat landraces were analysed using genotype by sequencing (GBS) arrays containing ~10 K unique markers. Pair-wise genetic distance analyses revealed significant genetic distances between landraces, particularly among those collected from distanced provinces. From these analyses, we were able to divide the landraces into 14 major classes, with the greatest degree of diversity evident among landraces isolated from Badakhshan province. Population-based analyses revealed an additional 15 sub-populations within our germplasm, and significant correlations were evident in both the provincial and botanical varieties. Genetic distance analysis was used to identify differences among provinces, with the strongest correlations seen between landraces from Herat and Ghor province, followed closely by those between Badakhshan and Takhar provinces. This result closely resembles existing agro-climatic zones within Afghanistan, as well as the wheat varieties commonly cultivated within these regions. Molecular variance analysis showed a higher proportion of intra-province variation among landraces compared with variation among all landraces as a whole. CONCLUSION The SNP analyses presented here highlight the importance and genetic diversity of Afghan wheat landraces. Furthermore, these data strongly refute a previous analysis that suggested low genetic diverse within this germplasm. Ongoing analyses include phenotypic characterisation of these landraces to identify functional traits associated with individual genotypes. Taken together, these analyses can be used to help improve wheat cultivation in Afghanistan, while providing insights into the evolution and selective pressures underlying these distinct landraces.
Collapse
Affiliation(s)
- Alagu Manickavelu
- />Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813 Japan
| | - Abdulqader Jighly
- />International Centre for Agricultural Research in the Dry Areas (ICARDA), P. O. Box 5466, Aleppo, Syria
| | - Tomohiro Ban
- />Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813 Japan
| |
Collapse
|
41
|
Dao A, Sanou J, Mitchell SE, Gracen V, Danquah EY. Genetic diversity among INERA maize inbred lines with single nucleotide polymorphism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines. BMC Genet 2014; 15:127. [PMID: 25421948 PMCID: PMC4253617 DOI: 10.1186/s12863-014-0127-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 11/05/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic diversity provides the capacity for plants to meet changing environments. It is fundamentally important in crop improvement. Fifty-nine local maize lines developed at INERA and 41 exotic (temperate and tropical) inbred lines were characterized using 1057 SNP markers to (1) analyse the genetic diversity in a diverse set of maize inbred lines; (2) determine the level of genetic diversity in INERA inbred lines and patterns of relationships of these inbred lines developed from two sources; and (3) examine the genetic differences between local and exotic germplasms. RESULTS Roger's genetic distance for about 64% of the pairs of lines fell between 0.300 and 0.400. Sixty one per cent of the pairs of lines also showed relative kinship values of zero. Model-based population structure analysis and principal component analysis revealed the presence of 5 groups that agree, to some extent, with the origin of the germplasm. There was genetic diversity among INERA inbred lines, which were genetically less closely related and showed a low level of heterozygosity. These lines could be divided into 3 major distinct groups and a mixed group consistent with the source population of the lines. Pairwise comparisons between local and exotic germplasms showed that the temperate and some IITA lines were differentiated from INERA lines. There appeared to be substantial levels of genetic variation between local and exotic germplasms as revealed by missing and unique alleles. CONCLUSIONS Allelic frequency differences observed between the germplasms, together with unique alleles identified within each germplasm, shows the potential for a mutual improvement between the sets of germplasm. The results from this study will be useful to breeders in designing inbred-hybrid breeding programs, association mapping population studies and marker assisted breeding.
Collapse
Affiliation(s)
- Abdalla Dao
- Institute of Environment and Agricultural Research (INERA), BP 910, Bobo-Dioulasso, Burkina Faso.
| | - Jacob Sanou
- Institute of Environment and Agricultural Research (INERA), BP 910, Bobo-Dioulasso, Burkina Faso.
| | - Sharon E Mitchell
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - Vernon Gracen
- Department of Plant Breeding and Genetics, 520 Bradfield Hall, Cornell University, Ithaca, NY, 14850, USA.
| | - Eric Y Danquah
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, BMP 30, Accra, Legon, Ghana.
| |
Collapse
|
42
|
de Oliveira EJ, Ferreira CF, da Silva Santos V, de Jesus ON, Oliveira GAF, da Silva MS. Potential of SNP markers for the characterization of Brazilian cassava germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1423-40. [PMID: 24737135 DOI: 10.1007/s00122-014-2309-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 03/31/2014] [Indexed: 05/20/2023]
Abstract
High-throughput markers, such as SNPs, along with different methodologies were used to evaluate the applicability of the Bayesian approach and the multivariate analysis in structuring the genetic diversity in cassavas. The objective of the present work was to evaluate the diversity and genetic structure of the largest cassava germplasm bank in Brazil. Complementary methodological approaches such as discriminant analysis of principal components (DAPC), Bayesian analysis and molecular analysis of variance (AMOVA) were used to understand the structure and diversity of 1,280 accessions genotyped using 402 single nucleotide polymorphism markers. The genetic diversity (0.327) and the average observed heterozygosity (0.322) were high considering the bi-allelic markers. In terms of population, the presence of a complex genetic structure was observed indicating the formation of 30 clusters by DAPC and 34 clusters by Bayesian analysis. Both methodologies presented difficulties and controversies in terms of the allocation of some accessions to specific clusters. However, the clusters suggested by the DAPC analysis seemed to be more consistent for presenting higher probability of allocation of the accessions within the clusters. Prior information related to breeding patterns and geographic origins of the accessions were not sufficient for providing clear differentiation between the clusters according to the AMOVA analysis. In contrast, the F ST was maximized when considering the clusters suggested by the Bayesian and DAPC analyses. The high frequency of germplasm exchange between producers and the subsequent alteration of the name of the same material may be one of the causes of the low association between genetic diversity and geographic origin. The results of this study may benefit cassava germplasm conservation programs, and contribute to the maximization of genetic gains in breeding programs.
Collapse
|
43
|
Westengen OT, Ring KH, Berg PR, Brysting AK. Modern maize varieties going local in the semi-arid zone in Tanzania. BMC Evol Biol 2014; 14:1. [PMID: 24382122 PMCID: PMC3890540 DOI: 10.1186/1471-2148-14-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 12/18/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Maize is the most produced crop in Sub-Saharan Africa, but yields are low and climate change is projected to further constrain smallholder production. The current efforts to breed and disseminate new high yielding and climate ready maize varieties are implemented through the formal seed system; the chain of public and private sector activities and institutions that produce and release certified seeds. These efforts are taking place in contexts currently dominated by informal seed systems; local and informal seed management and exchange channels with a long history of adapting crops to local conditions. We here present a case study of the genetic effects of both formal and informal seed management from the semi-arid zone in Tanzania. RESULTS Two open pollinated varieties (OPVs), Staha and TMV1, first released by the formal seed system in the 1980s are cultivated on two-thirds of the maize fields among the surveyed households. Farmer-recycling of improved varieties and seed selection are common on-farm seed management practices. Drought tolerance and high yield are the most important characteristics reported as reason for cultivating the current varieties as well as the most important criteria for farmers' seed selection. Bayesian cluster analysis, PCA and FST analyses based on 131 SNPs clearly distinguish between the two OPVs, and despite considerable heterogeneity between and within seed lots, there is insignificant differentiation between breeder's seeds and commercial seeds in both OPVs. Genetic separation increases as the formal system varieties enter the informal system and both hybridization with unrelated varieties and directional selection probably play a role in the differentiation. Using a Bayesian association approach we identify three loci putatively under selection in the informal seed system. CONCLUSIONS Our results suggest that the formal seed system in the study area distributes seed lots that are true to type. We suggest that hybridization and directional selection differentiate farmer recycled seed lots from the original varieties and potentially lead to beneficial creolization. Access to drought tolerant OPVs in combination with farmer seed selection is likely to enhance seed system security and farmers' adaptive capacity in the face of climate change.
Collapse
Affiliation(s)
- Ola T Westengen
- Centre for Development and the Environment (SUM), University of Oslo, Box 1166 Blindern, NO-0317 Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Kristoffer H Ring
- Centre for Development and the Environment (SUM), University of Oslo, Box 1166 Blindern, NO-0317 Oslo, Norway
| | - Paul R Berg
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Anne K Brysting
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Box 1066 Blindern, NO-0316 Oslo, Norway
| |
Collapse
|
44
|
Thirunavukkarasu N, Hossain F, Shiriga K, Mittal S, Arora K, Rathore A, Mohan S, Shah T, Sharma R, Namratha PM, Mithra ASV, Mohapatra T, Gupta HS. Unraveling the genetic architecture of subtropical maize (Zea mays L.) lines to assess their utility in breeding programs. BMC Genomics 2013; 14:877. [PMID: 24330649 PMCID: PMC3867671 DOI: 10.1186/1471-2164-14-877] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 12/10/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Maize is an increasingly important food crop in southeast Asia. The elucidation of its genetic architecture, accomplished by exploring quantitative trait loci and useful alleles in various lines across numerous breeding programs, is therefore of great interest. The present study aimed to characterize subtropical maize lines using high-quality SNPs distributed throughout the genome. RESULTS We genotyped a panel of 240 subtropical elite maize inbred lines and carried out linkage disequilibrium, genetic diversity, population structure, and principal component analyses on the generated SNP data. The mean SNP distance across the genome was 70 Kb. The genome had both high and low linkage disequilibrium (LD) regions; the latter were dominant in areas near the gene-rich telomeric portions where recombination is frequent. A total of 252 haplotype blocks, ranging in size from 1 to 15.8 Mb, were identified. Slow LD decay (200-300 Kb) at r(2) ≤ 0.1 across all chromosomes explained the selection of favorable traits around low LD regions in different breeding programs. The association mapping panel was characterized by strong population substructure. Genotypes were grouped into three distinct clusters with a mean genetic dissimilarity coefficient of 0.36. CONCLUSIONS The genotyped panel of subtropical maize lines characterized in this study should be useful for association mapping of agronomically important genes. The dissimilarity uncovered among genotypes provides an opportunity to exploit the heterotic potential of subtropical elite maize breeding lines.
Collapse
|
45
|
Zea mays (L.) P1 locus for cob glume color identified as a post-domestication selection target with an effect on temperate maize genomes. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.cj.2013.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
46
|
Van K, Kang YJ, Han KS, Lee YH, Gwag JG, Moon JK, Lee SH. Genome-wide SNP discovery in mungbean by Illumina HiSeq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2017-27. [PMID: 23674132 DOI: 10.1007/s00122-013-2114-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 04/20/2013] [Indexed: 05/08/2023]
Abstract
Mungbean [Vigna radiata (L.) Wilczek], a self-pollinated diploid plant with 2n = 22 chromosomes, is an important legume crop with a high-quality amino acid profile. Sequence variation at the whole-genome level was examined by comparing two mungbean cultivars, Sunhwanokdu and Gyeonggijaerae 5, using Illumina HiSeq sequencing data. More than 40 billion bp from both mungbean cultivars were sequenced to a depth of 72×. After de novo assembly of Sunhwanokdu contigs by ABySS 1.3.2 (N50 = 9,958 bp), those longer than 10 kb were aligned with Gyeonggijaerae 5 reads using the Burrows-Wheeler Aligner. SAMTools was used for retrieving single nucleotide polymorphisms (SNPs) between Sunhwanokdu and Gyeonggijaerae 5, defining the lowest and highest depths as 5 and 100, respectively, and the sequence quality as 100. Of the 305,504 single-base changes identified, 40,503 SNPs were considered heterozygous in Gyeonggijaerae 5. Among the remaining 265,001 SNPs, 65.9 % (174,579 cases) were transitions and 34.1 % (90,422 cases) were transversions. For SNP validation, a total of 42 SNPs were chosen among Sunhwanokdu contigs longer than 10 kb and sharing at least 80 % sequence identity with common bean expressed sequence tags as determined with est2genome. Using seven mungbean cultivars from various origins in addition to Sunhwanokdu and Gyeonggijaerae 5, most of the SNPs identified by bioinformatics tools were confirmed by Sanger sequencing. These genome-wide SNP markers could enrich the current molecular resources and might be of value for the construction of a mungbean genetic map and the investigation of genetic diversity.
Collapse
Affiliation(s)
- Kyujung Van
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | | | | | | | | | | | | |
Collapse
|
47
|
Semagn K, Beyene Y, Makumbi D, Mugo S, Prasanna BM, Magorokosho C, Atlin G. Quality control genotyping for assessment of genetic identity and purity in diverse tropical maize inbred lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1487-501. [PMID: 22801872 DOI: 10.1007/s00122-012-1928-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 06/16/2012] [Indexed: 05/20/2023]
Abstract
Quality control (QC) genotyping is an important component in breeding, but to our knowledge there are not well established protocols for its implementation in practical breeding programs. The objectives of our study were to (a) ascertain genetic identity among 2-4 seed sources of the same inbred line, (b) evaluate the extent of genetic homogeneity within inbred lines, and (c) identify a subset of highly informative single-nucleotide polymorphism (SNP) markers for routine and low-cost QC genotyping and suggest guidelines for data interpretation. We used a total of 28 maize inbred lines to study genetic identity among different seed sources by genotyping them with 532 and 1,065 SNPs using the KASPar and GoldenGate platforms, respectively. An additional set of 544 inbred lines was used for studying genetic homogeneity. The proportion of alleles that differed between seed sources of the same inbred line varied from 0.1 to 42.3 %. Seed sources exhibiting high levels of genetic distance are mis-labeled, while those with lower levels of difference are contaminated or still segregating. Genetic homogeneity varied from 68.7 to 100 % with 71.3 % of the inbred lines considered to be homogenous. Based on the data sets obtained for a wide range of sample sizes and diverse genetic backgrounds, we recommended a subset of 50-100 SNPs for routine and low-cost QC genotyping, verified them in a different set of double haploid and inbred lines, and outlined a protocol that could be used to minimize errors in genetic analyses and breeding.
Collapse
Affiliation(s)
- Kassa Semagn
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P.O. Box 1041, Nairobi, 00621, Kenya.
| | | | | | | | | | | | | |
Collapse
|