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Aghogho CI, Kayondo SI, Maziya-Dixon B, Eleblu SJ, Asante I, Offei SK, Parkes E, Ikpan Smith A, Adesokan M, Abioye R, Chijioke U, Ogunpaimo K, Kulakow P, Egesi C, Dufour D, Rabbi IY. Exploring genetic variability, heritability, and trait correlations in gari and eba quality from diverse cassava varieties in Nigeria. J Sci Food Agric 2023. [PMID: 37515474 DOI: 10.1002/jsfa.12889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 07/10/2023] [Accepted: 07/29/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND Gari (especially in Nigeria) is an important West African food product made from cassava. It is an affordable, precooked, dry, easy to prepare and store food product. Eba is a stiff dough produced by reconstituting gari in hot water. Gari and eba quality is an important driver of varietal acceptance by farmers, processors, and consumers. RESULTS This study characterized the genetic variability, heritability, and correlations among quality-related traits of fresh roots, gari, and eba. Thirty-three diverse genotypes, including landraces and released and advanced breeding genotypes, were used in this study. In total, 40 traits categorized into fresh root quality, colour, functional, and texture properties trait groups were assessed. We observed broad phenotypic variability among the genotypes used in this study. Dry matter content had a positive (P < 0.05) correlation with gari%, bulk density and a negative correlation with eba hardness and gumminess. Broad-sense heritability across all environments varied considerably among the different trait groups: 62% to 79% for fresh root quality, 0% to 96% for colour, 0% to 79% for functional and 0% to 57% for texture properties. CONCLUSIONS The stable broad-sense heritability found for gari%, gari and eba colour, bulk density, swelling index, and hardness measured using instrumental texture profile analysis coupled with sufficient variability in the population indicate good potential for genetic improvement of these traits through recurrent selection. Also, it is possible to genetically improve gari%, bulk density, and swelling power by simultaneously improving the dry matter content of fresh roots. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Cynthia Idhigu Aghogho
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences University of Ghana, Legon Boundary, Accra, Ghana
- International Institute of Tropical Agriculture (IITA) PMB 5320, Ibadan, Nigeria
| | - Siraj Ismail Kayondo
- International Institute of Tropical Agriculture (IITA) PMB 5320, Ibadan, Nigeria
| | - Bussie Maziya-Dixon
- International Institute of Tropical Agriculture (IITA) PMB 5320, Ibadan, Nigeria
| | - Saviour Jy Eleblu
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences University of Ghana, Legon Boundary, Accra, Ghana
| | - Isaac Asante
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences University of Ghana, Legon Boundary, Accra, Ghana
| | - Samuel K Offei
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences University of Ghana, Legon Boundary, Accra, Ghana
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture (IITA) PMB 5320, Ibadan, Nigeria
| | - Andrew Ikpan Smith
- International Institute of Tropical Agriculture (IITA) PMB 5320, Ibadan, Nigeria
| | - Micheal Adesokan
- International Institute of Tropical Agriculture (IITA) PMB 5320, Ibadan, Nigeria
| | - Racheal Abioye
- International Institute of Tropical Agriculture (IITA) PMB 5320, Ibadan, Nigeria
| | - Ugo Chijioke
- National Root Crops Research Institute, Umudike, Nigeria
| | - Kayode Ogunpaimo
- International Institute of Tropical Agriculture (IITA) PMB 5320, Ibadan, Nigeria
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA) PMB 5320, Ibadan, Nigeria
| | - Chiedozie Egesi
- National Root Crops Research Institute, Umudike, Nigeria
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Dominique Dufour
- CIRAD, UMR Qualisud, Montpellier, France
- Qualisud, Université Montpellier, CIRAD, Montpellier SupAgro, Université d'Avignon, Université de La Réunion, Montpellier, France
| | - Ismail Y Rabbi
- International Institute of Tropical Agriculture (IITA) PMB 5320, Ibadan, Nigeria
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Rodrmguez EPB, Morante N, Salazar S, Hyde PT, Setter TL, Kulakow P, Aparicio JS, Zhang X. Flower-inducing technology facilitates speed breeding in cassava. Front Plant Sci 2023; 14:1172056. [PMID: 37284728 PMCID: PMC10239864 DOI: 10.3389/fpls.2023.1172056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/13/2023] [Indexed: 06/08/2023]
Abstract
Cassava is a tropical crop that provides daily carbohydrates to more than 800 million people. New cassava cultivars with improved yield, disease resistance, and food quality are critical to end hunger and reduce poverty in the tropics. However, the progress of new cultivar development has been dragged down by difficulties obtaining flowers from desired parental plants to enable designed crosses. Inducing early flowering and increasing seed production are crucial to improving the efficiency of developing farmer-preferred cultivars. In the present study, we used breeding progenitors to evaluate the effectiveness of flower-inducing technology, including photoperiod extension, pruning, and plant growth regulators. Photoperiod extension significantly reduced the time to flowering in all 150 breeding progenitors, especially late-flowering progenitors which were reduced from 6-7 months to 3-4 months. Seed production was increased by using the combination of pruning and plant growth regulators. Combining photoperiod extension with pruning and the PGR 6-benzyladenine (synthetic cytokinin) produced significantly more fruits and seeds than only photoperiod extension and pruning. Another growth regulator, silver thiosulfate, commonly used to block the action of ethylene, did not show a significant effect on fruit or seed production when combined with pruning. The present study validated a protocol for flower induction in cassava breeding programs and discussed factors to consider in implementing the technology. By inducing early flowering and increasing seed production, the protocol helped move one step further for speed breeding in cassava.
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Affiliation(s)
| | - Nelson Morante
- Cassava Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Sandra Salazar
- Cassava Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Peter T. Hyde
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Tim L. Setter
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Peter Kulakow
- Cassava Program, International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Xiaofei Zhang
- Cassava Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Aghogho CI, Eleblu SJY, Bakare MA, Kayondo IS, Asante I, Parkes EY, Kulakow P, Offei SK, Rabbi I. Genetic variability and genotype by environment interaction of two major cassava processed products in multi-environments. Front Plant Sci 2022; 13:974795. [PMID: 36325542 PMCID: PMC9618686 DOI: 10.3389/fpls.2022.974795] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Conversion of cassava (Manihot esculenta) roots to processed products such as gari and fufu before consumption is a common practice worldwide by cassava end-user for detoxification, prolonged shelf life or profitability. Fresh root and processed product yield are supposed to be equivalent for each genotype, however, that is not the case. Developing genotypes with high product conversion rate is an important breeding goal in cassava as it drives the adoption rates of new varieties. The objective of this study was to quantify the contribution of genetic and genotype-by-environment interaction (GEI) patterns on cassava root conversion rate to gari and fufu. Sixty-seven advanced breeding genotypes from the International Institute of Tropical Agriculture (IITA) were evaluated across eight environments in Nigeria. Root conversion rate means across trials ranges from 14.72 to 22.76% for gari% and 16.96-24.24% for fufu%. Heritability estimates range from 0.17 to 0.74 for trial bases and 0.71 overall environment for gari% and 0.03-0.65 for trial bases and 0.72 overall environment for fufu% which implies that genetic improvement can be made on these traits. Root conversion rate for both gari and fufu% showed a negative but insignificant correlation with fresh root yield and significant positive correlation to Dry Matter content. For all fitted models, environment and interaction had explained more of the phenotypic variation observed among genotypes for both product conversion rates showing the presence of a strong GEI. Wrickle ecovalence (Wi) stability analysis and Geometric Adaptability index (GAI) identified G40 (TMS14F1285P0006) as part of top 5 genotypes for gari% but no overlapping genotype was identified by both stability analysis for fufu%. This genotypic performance across environments suggests that it is possible to have genotype with dual-purpose for high gari and fufu conversion rate.
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Affiliation(s)
- Cynthia Idhigu Aghogho
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences University of Ghana, Legon, Ghana
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Saviour J. Y. Eleblu
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences University of Ghana, Legon, Ghana
| | - Moshood A. Bakare
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
| | | | - Isaac Asante
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences University of Ghana, Legon, Ghana
| | | | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Samuel Kwame Offei
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences University of Ghana, Legon, Ghana
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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Ige AD, Olasanmi B, Bauchet GJ, Kayondo IS, Mbanjo EGN, Uwugiaren R, Motomura-Wages S, Norton J, Egesi C, Parkes EY, Kulakow P, Ceballos H, Dieng I, Rabbi IY. Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content. Front Plant Sci 2022; 13:1016170. [PMID: 36311140 PMCID: PMC9597466 DOI: 10.3389/fpls.2022.1016170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness common among pre-school children and pregnant women in developing countries particularly Africa. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. Single nucleotide polymorphism (SNP) markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for routine marker-assisted selection (MAS). This is due to the lack of useful information on markers' performances in diverse genetic backgrounds. To overcome this bottleneck, technical and biological validation of the loci associated with increased carotenoid content and dry matter content were carried out using populations independent of the marker discovery population. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific polymerase chain reaction (PCR) assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r< 0.40) due to the more quantitative nature of the trait. This work confirmed the markers' effectiveness in multiple backgrounds, therefore, further strengthening their value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker validation, thus leading to the more routine use of markers in MAS in cassava improvement programs.
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Affiliation(s)
- Adenike D. Ige
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
- Pan African University Life and Earth Sciences Institute (including Health and Agriculture), University of Ibadan, Ibadan, Nigeria
| | - Bunmi Olasanmi
- Department of Crop and Horticultural Sciences, University of Ibadan, Ibadan, Nigeria
| | | | - Ismail S. Kayondo
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | | | - Ruth Uwugiaren
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
- Molecular Plant Sciences program, Washington State University, Pullman, WA, United States
| | - Sharon Motomura-Wages
- College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Hilo, HI, United States
| | - Joanna Norton
- College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Hilo, HI, United States
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
- Cornell University, Ithaca, NY, United States
| | - Elizabeth Y. Parkes
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Hernán Ceballos
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Ibnou Dieng
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Ismail Y. Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
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5
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Joseph Fernando EA, Selvaraj MG, Delgado A, Rabbi I, Kulakow P. Frontline remote sensing tool to locate hidden traits in root and tuber crops. Mol Plant 2022; 15:1500-1502. [PMID: 36045578 DOI: 10.1016/j.molp.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/19/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Ezhilmathi Angela Joseph Fernando
- The Alliance of Bioversity International and International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, Apartado Aereo 6713, Cali 763537, Colombia.
| | - Michael Gomez Selvaraj
- The Alliance of Bioversity International and International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, Apartado Aereo 6713, Cali 763537, Colombia
| | - Alfredo Delgado
- IDS GeoRadar North America, 14818 West 6th Avenue, Unit 1-A Golden, Colorado 80401, USA
| | - Ismail Rabbi
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Oyo State 200001, Nigeria
| | - Peter Kulakow
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Oyo State 200001, Nigeria
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6
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Bakare MA, Kayondo SI, Aghogho CI, Wolfe MD, Parkes EY, Kulakow P, Egesi C, Jannink JL, Rabbi IY. Parsimonious genotype by environment interaction covariance models for cassava ( Manihot esculenta). Front Plant Sci 2022; 13:978248. [PMID: 36212387 PMCID: PMC9532941 DOI: 10.3389/fpls.2022.978248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
The assessment of cassava clones across multiple environments is often carried out at the uniform yield trial, a late evaluation stage, before variety release. This is to assess the differential response of the varieties across the testing environments, a phenomenon referred to as genotype-by-environment interaction (GEI). This phenomenon is considered a critical challenge confronted by plant breeders in developing crop varieties. This study used the data from variety trials established as randomized complete block design (RCBD) in three replicates across 11 locations in different agro-ecological zones in Nigeria over four cropping seasons (2016-2017, 2017-2018, 2018-2019, and 2019-2020). We evaluated a total of 96 varieties, including five checks, across 48 trials. We exploited the intricate pattern of GEI by fitting variance-covariance structure models on fresh root yield. The goodness-of-fit statistics revealed that the factor analytic model of order 3 (FA3) is the most parsimonious model based on Akaike Information Criterion (AIC). The three-factor loadings from the FA3 model explained, on average across the 27 environments, 53.5% [FA (1)], 14.0% [FA (2)], and 11.5% [FA (3)] of the genetic effect, and altogether accounted for 79.0% of total genetic variability. The association of factor loadings with weather covariates using partial least squares regression (PLSR) revealed that minimum temperature, precipitation and relative humidity are weather conditions influencing the genotypic response across the testing environments in the southern region and maximum temperature, wind speed, and temperature range for those in the northern region of Nigeria. We conclude that the FA3 model identified the common latent factors to dissect and account for complex interaction in multi-environment field trials, and the PLSR is an effective approach for describing GEI variability in the context of multi-environment trials where external environmental covariables are included in modeling.
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Affiliation(s)
- Moshood A. Bakare
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Cynthia I. Aghogho
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Marnin D. Wolfe
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- Department of Crop, Soil and Environmental Sciences, College of Agriculture, Auburn University, Auburn, AL, United States
| | | | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Chiedozie Egesi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI), Umudike, Umuahia, Nigeria
| | - Jean-Luc Jannink
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
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7
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Bakare MA, Kayondo SI, Aghogho CI, Wolfe MD, Parkes EY, Kulakow P, Egesi C, Rabbi IY, Jannink JL. Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methods. PLoS One 2022; 17:e0268189. [PMID: 35849556 PMCID: PMC9292083 DOI: 10.1371/journal.pone.0268189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/23/2022] [Indexed: 11/19/2022] Open
Abstract
Variety advancement decisions for root quality and yield-related traits in cassava are complex due to the variable patterns of genotype-by-environment interactions (GEI). Therefore, studies focused on the dissection of the existing patterns of GEI using linear-bilinear models such as Finlay-Wilkinson (FW), additive main effect and multiplicative interaction (AMMI), and genotype and genotype-by-environment (GGE) interaction models are critical in defining the target population of environments (TPEs) for future testing, selection, and advancement. This study assessed 36 elite cassava clones in 11 locations over three cropping seasons in the cassava breeding program of IITA based in Nigeria to quantify the GEI effects for root quality and yield-related traits. Genetic correlation coefficients and heritability estimates among environments found mostly intermediate to high values indicating high correlations with the major TPE. There was a differential clonal ranking among the environments indicating the existence of GEI as also revealed by the likelihood ratio test (LRT), which further confirmed the statistical model with the heterogeneity of error variances across the environments fit better. For all fitted models, we found the main effects of environment, genotype, and interaction significant for all observed traits except for dry matter content whose GEI sensitivity was marginally significant as found using the FW model. We identified TMS14F1297P0019 and TMEB419 as two topmost stable clones with a sensitivity values of 0.63 and 0.66 respectively using the FW model. However, GGE and AMMI stability value in conjunction with genotype selection index revealed that IITA-TMS-IBA000070 and TMS14F1036P0007 were the top-ranking clones combining both stability and yield performance measures. The AMMI-2 model clustered the testing environments into 6 mega-environments based on winning genotypes for fresh root yield. Alternatively, we identified 3 clusters of testing environments based on genotypic BLUPs derived from the random GEI component.
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Affiliation(s)
- Moshood A. Bakare
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States of America
- * E-mail: (J-LJ); (MAB)
| | | | - Cynthia I. Aghogho
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Marnin D. Wolfe
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States of America
| | | | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Chiedozie Egesi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States of America
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- National Root Crops Research Institute Umudike, Umuahia, Nigeria
| | | | - Jean-Luc Jannink
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States of America
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States of America
- * E-mail: (J-LJ); (MAB)
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Morales N, Ogbonna AC, Ellerbrock BJ, Bauchet GJ, Tantikanjana T, Tecle IY, Powell AF, Lyon D, Menda N, Simoes CC, Saha S, Hosmani P, Flores M, Panitz N, Preble RS, Agbona A, Rabbi I, Kulakow P, Peteti P, Kawuki R, Esuma W, Kanaabi M, Chelangat DM, Uba E, Olojede A, Onyeka J, Shah T, Karanja M, Egesi C, Tufan H, Paterne A, Asfaw A, Jannink JL, Wolfe M, Birkett CL, Waring DJ, Hershberger JM, Gore MA, Robbins KR, Rife T, Courtney C, Poland J, Arnaud E, Laporte MA, Kulembeka H, Salum K, Mrema E, Brown A, Bayo S, Uwimana B, Akech V, Yencho C, de Boeck B, Campos H, Swennen R, Edwards JD, Mueller LA. Breedbase: a digital ecosystem for modern plant breeding. G3 Genes|Genomes|Genetics 2022; 12:6564228. [PMID: 35385099 PMCID: PMC9258556 DOI: 10.1093/g3journal/jkac078] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/14/2022] [Indexed: 01/17/2023]
Abstract
Modern breeding methods integrate next-generation sequencing and phenomics to identify plants with the best characteristics and greatest genetic merit for use as parents in subsequent breeding cycles to ultimately create improved cultivars able to sustain high adoption rates by farmers. This data-driven approach hinges on strong foundations in data management, quality control, and analytics. Of crucial importance is a central database able to (1) track breeding materials, (2) store experimental evaluations, (3) record phenotypic measurements using consistent ontologies, (4) store genotypic information, and (5) implement algorithms for analysis, prediction, and selection decisions. Because of the complexity of the breeding process, breeding databases also tend to be complex, difficult, and expensive to implement and maintain. Here, we present a breeding database system, Breedbase (https://breedbase.org/, last accessed 4/18/2022). Originally initiated as Cassavabase (https://cassavabase.org/, last accessed 4/18/2022) with the NextGen Cassava project (https://www.nextgencassava.org/, last accessed 4/18/2022), and later developed into a crop-agnostic system, it is presently used by dozens of different crops and projects. The system is web based and is available as open source software. It is available on GitHub (https://github.com/solgenomics/, last accessed 4/18/2022) and packaged in a Docker image for deployment (https://hub.docker.com/u/breedbase, last accessed 4/18/2022). The Breedbase system enables breeding programs to better manage and leverage their data for decision making within a fully integrated digital ecosystem.
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Affiliation(s)
- Nicolas Morales
- Boyce Thompson Institute , Ithaca, NY 14853, USA
- Cornell University , Ithaca, NY 14853, USA
| | - Alex C Ogbonna
- Boyce Thompson Institute , Ithaca, NY 14853, USA
- Cornell University , Ithaca, NY 14853, USA
| | | | | | | | | | | | - David Lyon
- Boyce Thompson Institute , Ithaca, NY 14853, USA
| | - Naama Menda
- Boyce Thompson Institute , Ithaca, NY 14853, USA
| | | | - Surya Saha
- Boyce Thompson Institute , Ithaca, NY 14853, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Ezenwanyi Uba
- National Root Crops Research Institute (NRCRI) , 463109 Umudike, Nigeria
| | - Adeyemi Olojede
- National Root Crops Research Institute (NRCRI) , 463109 Umudike, Nigeria
| | - Joseph Onyeka
- National Root Crops Research Institute (NRCRI) , 463109 Umudike, Nigeria
| | | | | | - Chiedozie Egesi
- Boyce Thompson Institute , Ithaca, NY 14853, USA
- IITA Ibadan , 200001 Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI) , 463109 Umudike, Nigeria
| | - Hale Tufan
- Cornell University , Ithaca, NY 14853, USA
| | | | | | - Jean-Luc Jannink
- Cornell University , Ithaca, NY 14853, USA
- USDA-ARS , Ithaca, NY 14853, USA
| | | | - Clay L Birkett
- Cornell University , Ithaca, NY 14853, USA
- USDA-ARS , Ithaca, NY 14853, USA
| | - David J Waring
- Cornell University , Ithaca, NY 14853, USA
- USDA-ARS , Ithaca, NY 14853, USA
| | | | | | | | - Trevor Rife
- Kansas State University , Manhattan, KS 66506, USA
| | | | - Jesse Poland
- Kansas State University , Manhattan, KS 66506, USA
| | | | | | | | | | | | | | | | | | | | - Craig Yencho
- North Carolina State University (NCSU) , Raleigh, NC 27695, USA
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9
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Rabbi IY, Kayondo SI, Bauchet G, Yusuf M, Aghogho CI, Ogunpaimo K, Uwugiaren R, Smith IA, Peteti P, Agbona A, Parkes E, Lydia E, Wolfe M, Jannink JL, Egesi C, Kulakow P. Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava. Plant Mol Biol 2022; 109:195-213. [PMID: 32734418 PMCID: PMC9162993 DOI: 10.1007/s11103-020-01038-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/20/2020] [Indexed: 05/05/2023]
Abstract
More than 40 QTLs associated with 14 stress-related, quality and agro-morphological traits were identified. A catalogue of favourable SNP markers for MAS and a list of candidate genes are provided. Cassava (Manihot esculenta) is one of the most important starchy root crops in the tropics due to its adaptation to marginal environments. Genetic progress in this clonally propagated crop can be accelerated through the discovery of markers and candidate genes that could be used in cassava breeding programs. We carried out a genome-wide association study (GWAS) using a panel of 5130 clones developed at the International Institute of Tropical Agriculture-Nigeria. The population was genotyped at more than 100,000 SNP markers via genotyping-by-sequencing (GBS). Genomic regions underlying genetic variation for 14 traits classified broadly into four categories: biotic stress (cassava mosaic disease and cassava green mite severity); quality (dry matter content and carotenoid content) and plant agronomy (harvest index and plant type) were investigated. We also included several agro-morphological traits related to leaves, stems and roots with high heritability. In total, 41 significant associations were uncovered. While some of the identified loci matched with those previously reported, we present additional association signals for the traits. We provide a catalogue of favourable alleles at the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in cassava breeding programs and candidate genes for functional validation.
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Affiliation(s)
- Ismail Yusuf Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria.
| | - Siraj Ismail Kayondo
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | | | - Muyideen Yusuf
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Cynthia Idhigu Aghogho
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Kayode Ogunpaimo
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Ruth Uwugiaren
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Ikpan Andrew Smith
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Prasad Peteti
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Afolabi Agbona
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Ezenwaka Lydia
- National Root Crops Research Institute (NRCRI), PMB 7006, Umudike, 440221, Nigeria
| | - Marnin Wolfe
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14850, USA
| | - Jean-Luc Jannink
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14850, USA
- United States Department of Agriculture - Agriculture Research Service, Ithaca, NY, 14850, USA
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
- National Root Crops Research Institute (NRCRI), PMB 7006, Umudike, 440221, Nigeria
- Global Development Department, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14850, USA
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
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10
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Oyetunde AK, Afolami SO, Kulakow P, Coyne D. The differential impact of four tropical species of root-knot nematodes (Meloidogyne spp.) on biofortified cassava. NEMATOLOGY 2022. [DOI: 10.1163/15685411-bja10161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Cassava plays an important food security role in Africa. Although a hardy crop in general, average yields are low, while traditional cultivars tend to be low in nutrients and vitamins. Substantial efforts have therefore been made to improve the nutritional quality of cassava through the development of biofortified cultivars. Although root-knot nematodes (RKN) are among the various important constraints affecting production, details on the impact of different species of RKN on cassava productivity are scarce. In this study, six popular cultivars of biofortified cassava were evaluated for their response to M. arenaria, M. enterolobii, M. incognita, M. javanica and a combination of all four species, in pots. All tested cultivars were susceptible to the four Meloidogyne species, but some cultivars showed a tolerance to M. arenaria infection. Galling damage was observed on feeder roots of inoculated plants, with nematode reproduction factors ranging between 2.3 and 9.5. Plant height, stem girth and fresh plant mass were significantly lower for most cultivars by as much as 70% following RKN infection. The highest root galling and damage were observed in plants following inoculation with a combination of the four species. As individual species inoculations, M. incognita and M. javanica were the most damaging, with the least damage observed in plants inoculated with M. arenaria only. These results confirm the pathogenicity of M. arenaria, M. incognita and M. javanica and further illustrate the potential of M. enterolobii to impact cassava production, while combined species infections demonstrate the greater levels of damage that these may cause.
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Affiliation(s)
- Aminat K. Oyetunde
- Department of Biological Sciences, Faculty of Science, Augustine University, P.M.B. 1010, Ilara-Epe 106101, Lagos State, Nigeria
- International Institute of Tropical Agriculture (IITA), Head Quarters and West Africa Hub, P.M.B. 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria
| | - Steve O. Afolami
- Department of Crop Protection, Federal University of Agriculture, P.M.B. 2240, Abeokuta, Ogun State, Nigeria
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Head Quarters and West Africa Hub, P.M.B. 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria
| | - Danny Coyne
- IITA, Kasarani, P.O. Box 30772-00100, Nairobi, Kenya
- Nematology Research Unit, Department of Biology, Ghent University, 9000 Gent, Belgium
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11
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Covarrubias-Pazaran G, Gebeyehu Z, Gemenet D, Werner C, Labroo M, Sirak S, Coaldrake P, Rabbi I, Kayondo SI, Parkes E, Kanju E, Mbanjo EGN, Agbona A, Kulakow P, Quinn M, Debaene J. Breeding Schemes: What Are They, How to Formalize Them, and How to Improve Them? Front Plant Sci 2022; 12:791859. [PMID: 35126417 PMCID: PMC8813775 DOI: 10.3389/fpls.2021.791859] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/10/2021] [Indexed: 05/26/2023]
Abstract
Formalized breeding schemes are a key component of breeding program design and a gateway to conducting plant breeding as a quantitative process. Unfortunately, breeding schemes are rarely defined, expressed in a quantifiable format, or stored in a database. Furthermore, the continuous review and improvement of breeding schemes is not routinely conducted in many breeding programs. Given the rapid development of novel breeding methodologies, it is important to adopt a philosophy of continuous improvement regarding breeding scheme design. Here, we discuss terms and definitions that are relevant to formalizing breeding pipelines, market segments and breeding schemes, and we present a software tool, Breeding Pipeline Manager, that can be used to formalize and continuously improve breeding schemes. In addition, we detail the use of continuous improvement methods and tools such as genetic simulation through a case study in the International Institute of Tropical Agriculture (IITA) Cassava east-Africa pipeline. We successfully deploy these tools and methods to optimize the program size as well as allocation of resources to the number of parents used, number of crosses made, and number of progeny produced. We propose a structured approach to improve breeding schemes which will help to sustain the rates of response to selection and help to deliver better products to farmers and consumers.
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Affiliation(s)
- Giovanny Covarrubias-Pazaran
- Excellence in Breeding Platform, Consultative Group on International Agricultural Research, Texcoco, Mexico
- Independent Researcher, Addis Ababa, Ethiopia
| | | | - Dorcus Gemenet
- Excellence in Breeding Platform, Consultative Group on International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Christian Werner
- Excellence in Breeding Platform, Consultative Group on International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Marlee Labroo
- Excellence in Breeding Platform, Consultative Group on International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Solomon Sirak
- Excellence in Breeding Platform, Consultative Group on International Agricultural Research, Texcoco, Mexico
| | - Peter Coaldrake
- Excellence in Breeding Platform, Consultative Group on International Agricultural Research, Texcoco, Mexico
| | - Ismail Rabbi
- International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Elizabeth Parkes
- International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Edward Kanju
- International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Afolabi Agbona
- International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Peter Kulakow
- International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Michael Quinn
- Excellence in Breeding Platform, Consultative Group on International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jan Debaene
- Excellence in Breeding Platform, Consultative Group on International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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12
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Nkouaya Mbanjo EG, Hershberger J, Peteti P, Agbona A, Ikpan A, Ogunpaimo K, Kayondo SI, Abioye RS, Nafiu K, Alamu EO, Adesokan M, Maziya-Dixon B, Parkes E, Kulakow P, Gore MA, Egesi C, Rabbi IY. Predicting starch content in cassava fresh roots using near-infrared spectroscopy. Front Plant Sci 2022; 13:990250. [PMID: 36426140 PMCID: PMC9679500 DOI: 10.3389/fpls.2022.990250] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/14/2022] [Indexed: 05/20/2023]
Abstract
The cassava starch market is promising in sub-Saharan Africa and increasing rapidly due to the numerous uses of starch in food industries. More accurate, high-throughput, and cost-effective phenotyping approaches could hasten the development of cassava varieties with high starch content to meet the growing market demand. This study investigated the effectiveness of a pocket-sized SCiO™ molecular sensor (SCiO) (740-1070 nm) to predict starch content in freshly ground cassava roots. A set of 344 unique genotypes from 11 field trials were evaluated. The predictive ability of individual trials was compared using partial least squares regression (PLSR). The 11 trials were aggregated to capture more variability, and the performance of the combined data was evaluated using two additional algorithms, random forest (RF) and support vector machine (SVM). The effect of pretreatment on model performance was examined. The predictive ability of SCiO was compared to that of two commercially available near-infrared (NIR) spectrometers, the portable ASD QualitySpec® Trek (QST) (350-2500 nm) and the benchtop FOSS XDS Rapid Content™ Analyzer (BT) (400-2490 nm). The heritability of NIR spectra was investigated, and important spectral wavelengths were identified. Model performance varied across trials and was related to the amount of genetic diversity captured in the trial. Regardless of the chemometric approach, a satisfactory and consistent estimate of starch content was obtained across pretreatments with the SCiO (correlation between the predicted and the observed test set, (R2 P): 0.84-0.90; ratio of performance deviation (RPD): 2.49-3.11, ratio of performance to interquartile distance (RPIQ): 3.24-4.08, concordance correlation coefficient (CCC): 0.91-0.94). While PLSR and SVM showed comparable prediction abilities, the RF model yielded the lowest performance. The heritability of the 331 NIRS spectra varied across trials and spectral regions but was highest (H2 > 0.5) between 871-1070 nm in most trials. Important wavelengths corresponding to absorption bands associated with starch and water were identified from 815 to 980 nm. Despite its limited spectral range, SCiO provided satisfactory prediction, as did BT, whereas QST showed less optimal calibration models. The SCiO spectrometer may be a cost-effective solution for phenotyping the starch content of fresh roots in resource-limited cassava breeding programs.
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Affiliation(s)
- Edwige Gaby Nkouaya Mbanjo
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
- *Correspondence: Edwige Gaby Nkouaya Mbanjo,
| | - Jenna Hershberger
- Department of Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC, United States
| | - Prasad Peteti
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Afolabi Agbona
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
- Molecular & Environmental Plant Sciences, Texas A&M University, College Station, TX, United States
| | - Andrew Ikpan
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Kayode Ogunpaimo
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Siraj Ismail Kayondo
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Racheal Smart Abioye
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Kehinde Nafiu
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | | | - Michael Adesokan
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Busie Maziya-Dixon
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Michael A. Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- National Root Crops Research Institute (NRCRI), Umuahia, Nigeria
| | - Ismail Yusuf Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
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13
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Wolfe MD, Chan AW, Kulakow P, Rabbi I, Jannink JL. Corrigendum to: Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices. Genetics 2021; 220:6489724. [PMID: 35100367 PMCID: PMC9097245 DOI: 10.1093/genetics/iyab225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Teeken B, Garner E, Agbona A, Balogun I, Olaosebikan O, Bello A, Madu T, Okoye B, Egesi C, Kulakow P, Tufan HA. Beyond “Women's Traits”: Exploring How Gender, Social Difference, and Household Characteristics Influence Trait Preferences. Front Sustain Food Syst 2021. [DOI: 10.3389/fsufs.2021.740926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Demand-led breeding strategies are gaining importance in public sector breeding globally. While borrowing approaches from the private sector, public sector programs remain mainly focused on food security and social impact related outcomes. This necessitates information on specific user groups and their preferences to build targeted customer and product profiles for informed breeding decisions. A variety of studies have identified gendered trait preferences, but do not systematically analyze differences related to or interactions of gender with other social dimensions, household characteristics, and geographic factors. This study integrates 1000minds survey trait trade-off analysis with the Rural Household Multi-Indicator Survey to study cassava trait preferences in Nigeria related to a major food product, gari. Results build on earlier research demonstrating that women prioritize food product quality traits while men prioritize agronomic traits. We show that food product quality traits are more important for members from food insecure households and gender differences between men and women increase among the food insecure. Furthermore, respondents from poorer households prioritize traits similar to respondents in non-poor households but there are notable trait differences between men and women in poor households. Women in female headed household prioritized quality traits more than women living with a spouse. Important regional differences in trait preferences were also observed. In the South East region, where household use of cassava is important, and connection to larger markets is less developed, quality traits and in ground storability were prioritized more than in other states. These results reinforce the importance of recognizing social difference and the heterogeneity among men and women, and how individual and household characteristics interact to reveal trait preference variability. This information can inform trait prioritization and guide development of breeding products that have higher social impact, which may ultimately serve the more vulnerable and align with development goals.
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15
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Wolfe MD, Chan AW, Kulakow P, Rabbi I, Jannink JL. Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices. Genetics 2021; 219:6363799. [PMID: 34740244 PMCID: PMC8570794 DOI: 10.1093/genetics/iyab122] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/13/2021] [Indexed: 11/14/2022] Open
Abstract
Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects, and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances, and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses was accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal the new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).
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Affiliation(s)
- Marnin D Wolfe
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Ariel W Chan
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Jean-Luc Jannink
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14850, USA.,USDA-ARS, Ithaca, NY 14850, USA
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16
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Esuma W, Ozimati A, Kulakow P, Gore MA, Wolfe MD, Nuwamanya E, Egesi C, Kawuki RS. Effectiveness of genomic selection for improving provitamin A carotenoid content and associated traits in cassava. G3 (Bethesda) 2021; 11:jkab160. [PMID: 33963852 PMCID: PMC8496257 DOI: 10.1093/g3journal/jkab160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/26/2021] [Indexed: 11/14/2022]
Abstract
Global efforts are underway to develop cassava with enhanced levels of provitamin A carotenoids to sustainably meet increasing demands for food and nutrition where the crop is a major staple. Herein, we tested the effectiveness of genomic selection (GS) for rapid improvement of cassava for total carotenoids content and associated traits. We evaluated 632 clones from Uganda's provitamin A cassava breeding pipeline and 648 West African introductions. At harvest, each clone was assessed for level of total carotenoids, dry matter content, and resistance to cassava brown streak disease (CBSD). All clones were genotyped with diversity array technology and imputed to a set of 23,431 single nucleotide polymorphic markers. We assessed predictive ability of four genomic prediction methods in scenarios of cross-validation, across population prediction, and inclusion of quantitative trait loci markers. Cross-validations produced the highest mean prediction ability for total carotenoids content (0.52) and the lowest for CBSD resistance (0.20), with G-BLUP outperforming other models tested. Across population, predictions showed low ability of Ugandan population to predict the performance of West African clones, with the highest predictive ability recorded for total carotenoids content (0.34) and the lowest for CBSD resistance (0.12) using G-BLUP. By incorporating chromosome 1 markers associated with carotenoids content as independent kernel in the G-BLUP model of a cross-validation scenario, prediction ability slightly improved from 0.52 to 0.58. These results reinforce ongoing efforts aimed at integrating GS into cassava breeding and demonstrate the utility of this tool for rapid genetic improvement.
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Affiliation(s)
- Williams Esuma
- National Crops Resources Research Institute, Kampala, Uganda
| | - Alfred Ozimati
- National Crops Resources Research Institute, Kampala, Uganda
| | - Peter Kulakow
- International Institute for Tropical Agriculture, Ibadan, Nigeria
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Marnin D Wolfe
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | | | - Chiedozie Egesi
- International Institute for Tropical Agriculture, Ibadan, Nigeria
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Robert S Kawuki
- National Crops Resources Research Institute, Kampala, Uganda
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17
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Oluwasanya D, Esan O, Hyde PT, Kulakow P, Setter TL. Flower Development in Cassava Is Feminized by Cytokinin, While Proliferation Is Stimulated by Anti-Ethylene and Pruning: Transcriptome Responses. Front Plant Sci 2021; 12:666266. [PMID: 34122486 PMCID: PMC8194492 DOI: 10.3389/fpls.2021.666266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/30/2021] [Indexed: 06/08/2023]
Abstract
Cassava, a tropical storage-root crop, is a major source of food security for millions in the tropics. Cassava breeding, however, is hindered by the poor development of flowers and a low ratio of female flowers to male flowers. To advance the understanding of the mechanistic factors regulating cassava flowering, combinations of plant growth regulators (PGRs) and pruning treatments were examined for their effectiveness in improving flower production and fruit set in field conditions. Pruning the fork-type branches, which arise at the shoot apex immediately below newly formed inflorescences, stimulated inflorescence and floral development. The anti-ethylene PGR silver thiosulfate (STS) also increased flower abundance. Both pruning and STS increased flower numbers while having minimal influence on sex ratios. In contrast, the cytokinin benzyladenine (BA) feminized flowers without increasing flower abundance. Combining pruning and STS treatments led to an additive increase in flower abundance; with the addition of BA, over 80% of flowers were females. This three-way treatment combination of pruning+STS+BA also led to an increase in fruit number. Transcriptomic analysis of gene expression in tissues of the apical region and developing inflorescence revealed that the enhancement of flower development by STS+BA was accompanied by downregulation of several genes associated with repression of flowering, including homologs of TEMPRANILLO1 (TEM1), GA receptor GID1b, and ABA signaling genes ABI1 and PP2CA. We conclude that flower-enhancing treatments with pruning, STS, and BA create widespread changes in the network of hormone signaling and regulatory factors beyond ethylene and cytokinin.
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Affiliation(s)
- Deborah Oluwasanya
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Cassava Breeding Unit, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Olayemisi Esan
- Cassava Breeding Unit, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Peter T. Hyde
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Peter Kulakow
- Cassava Breeding Unit, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Tim L. Setter
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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18
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Tize I, Fotso AK, Nukenine EN, Masso C, Ngome FA, Suh C, Lendzemo VW, Nchoutnji I, Manga G, Parkes E, Kulakow P, Kouebou C, Fiaboe KKM, Hanna R. New cassava germplasm for food and nutritional security in Central Africa. Sci Rep 2021; 11:7394. [PMID: 33795808 PMCID: PMC8016988 DOI: 10.1038/s41598-021-86958-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/22/2021] [Indexed: 11/08/2022] Open
Abstract
Cassava is a key food security crop in Central Africa, but its production depends largely on the use of local farmers' varieties characterized by inherently low yield which is compounded by generally high susceptibility to various growth and yield-limiting pests and diseases. Improved cassava genotypes have demonstrated the potential to substantially improve cassava's contribution to food security and the development of the cassava industry and the improvement of nutrition status elsewhere in Western Africa. Eleven improved cassava genotypes were compared with a local landrace (LMR) used as a check under field conditions over two years in eight locations, grouped in four agro-ecologies in Cameroon. Pest and disease abundance/incidence and damage severity were evaluated. At harvest, root yield and carotenoid content were measured. Best linear unbiased predictors showed the lowest breeding value for LMR with the cassava mosaic virus disease (+ 66.40 ± 2.42) compared with 1.00 ± 0.02% for the most susceptible improved genotype. Two genotypes (I010040-27 and I011797) stood out for having higher predicted fresh root yield means which were at least 16 times greater compared with LMR. Predicted total carotenoid content was the highest (+ 5.04 ± 0.17) for improved genotype I070593 compared with LMR which showed the lowest (- 3.90 ± 0.06%) and could contribute to the alleviation of vitamin A deficiency from cassava-based food systems. Diffusion of high-yielding and nutritious genotypes could alleviate food and nutritional security in Central Africa.
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Affiliation(s)
- Isaac Tize
- International Institute of Tropical Agriculture, BP 2008, Messa, Yaoundé, Cameroon
- Department of Biological Sciences, University of Ngaoundere, BP 454, Ngaoundere, Cameroon
| | - Apollin Kuate Fotso
- International Institute of Tropical Agriculture, BP 2008, Messa, Yaoundé, Cameroon.
| | - Elias Nchiwan Nukenine
- Department of Biological Sciences, University of Ngaoundere, BP 454, Ngaoundere, Cameroon
| | - Cargele Masso
- International Institute of Tropical Agriculture, BP 2008, Messa, Yaoundé, Cameroon
| | | | - Christopher Suh
- Institute of Agricultural Research for Development, BP 2067, Yaoundé, Cameroon
| | | | - Ibrahim Nchoutnji
- Institute of Agricultural Research for Development, BP 2067, Yaoundé, Cameroon
| | - Gabriel Manga
- Institute of Agricultural Research for Development, BP 2067, Yaoundé, Cameroon
| | - Elisabeth Parkes
- International Institute of Tropical Agriculture, PMB 320 Oyo Road, Ibadan, Nigeria
| | - Peter Kulakow
- International Institute of Tropical Agriculture, PMB 320 Oyo Road, Ibadan, Nigeria
| | - Christiant Kouebou
- Agricultural Investment and Market Development Project, Yaoundé, Cameroon
| | - Komi K M Fiaboe
- International Institute of Tropical Agriculture, BP 2008, Messa, Yaoundé, Cameroon
| | - Rachid Hanna
- International Institute of Tropical Agriculture, BP 2008, Messa, Yaoundé, Cameroon
- Congo Basin Institute, Institute of Environment and Sustainability, University of California, Box 951496, Los Angeles, USA
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19
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Teeken B, Agbona A, Bello A, Olaosebikan O, Alamu E, Adesokan M, Awoyale W, Madu T, Okoye B, Chijioke U, Owoade D, Okoro M, Bouniol A, Dufour D, Hershey C, Rabbi I, Maziya‐Dixon B, Egesi C, Tufan H, Kulakow P. Understanding cassava varietal preferences through pairwise ranking of gari-eba and fufu prepared by local farmer-processors. Int J Food Sci Technol 2021; 56:1258-1277. [PMID: 33776234 PMCID: PMC7984147 DOI: 10.1111/ijfs.14862] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 11/29/2022]
Abstract
Within communities in Osun and Imo States of Nigeria, farmer-processors grew and processed a diverse set of improved and landrace cassava varieties into the locally popular foods, gari, eba and fufu. Local and 15 main varieties were grown in a 'mother and baby trials' design in each state. Mother trials with three replications were processed by farmer-processors renown in their community for their processing skills. Baby trials were managed and processed by other farmer-processors. The objective was to identify food quality criteria to inform demand-led breeding to benefit users, especially women, given their key roles in processing. Farmer-processors evaluated the overall quality of fresh roots and derived food products through pairwise comparisons. Improved varieties had higher fresh and dry root yield. Overall, landraces ranked first for quality of gari and eba, but several improved varieties were also appreciated for good quality. Landraces in Osun had higher gari yield and a higher swelling power compared to improved varieties. Colour (browning), bulk density, swelling power, solubility and water absorption capacity were the criteria most related to food product ranking by farmer-processors. Evaluation of varieties under farmer-processors' conditions is crucial for providing guidance to breeders on critical selection criteria.
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Affiliation(s)
- Béla Teeken
- International Institute of Tropical AgricultureIbadanPMB 5320Nigeria
| | - Afolabi Agbona
- International Institute of Tropical AgricultureIbadanPMB 5320Nigeria
| | - Abolore Bello
- International Institute of Tropical AgricultureIbadanPMB 5320Nigeria
| | | | - Emmanuel Alamu
- International Institute of Tropical AgricultureIbadanPMB 5320Nigeria
| | - Michael Adesokan
- International Institute of Tropical AgricultureIbadanPMB 5320Nigeria
| | - Wasiu Awoyale
- International Institute of Tropical AgricultureIbadanPMB 5320Nigeria
| | - Tessy Madu
- International National Root Crops Research Institute (NRCRI)Umudike, UmuahiaPMB 7006Nigeria
| | - Benjamin Okoye
- International National Root Crops Research Institute (NRCRI)Umudike, UmuahiaPMB 7006Nigeria
| | - Ugo Chijioke
- International National Root Crops Research Institute (NRCRI)Umudike, UmuahiaPMB 7006Nigeria
- Department of Food Science & TechnologyKwara State UniversityMaleteKwara StatePMB 1530Nigeria
| | - Durodola Owoade
- International Institute of Tropical AgricultureIbadanPMB 5320Nigeria
| | - Maria Okoro
- International National Root Crops Research Institute (NRCRI)Umudike, UmuahiaPMB 7006Nigeria
| | - Alexandre Bouniol
- Laboratoire de Sciences des AlimentsFaculté des Sciences AgronomiquesUniversité d’Abomey‐CalaviJéricho03 BP 2819Benin
- CIRADUMR QUALISUDCotonou 01BP 526Benin
- QualisudCIRADMontpellier SupAgroUniversité d'AvignonUniversité de La RéunionUniversité MontpellierMontpellier, 34398France
| | - Dominique Dufour
- QualisudCIRADMontpellier SupAgroUniversité d'AvignonUniversité de La RéunionUniversité MontpellierMontpellier, 34398France
- CIRADUMR QUALISUDMontpellierF‐34398France
| | | | - Ismail Rabbi
- International Institute of Tropical AgricultureIbadanPMB 5320Nigeria
| | | | - Chiedozie Egesi
- International Institute of Tropical AgricultureIbadanPMB 5320Nigeria
- International National Root Crops Research Institute (NRCRI)Umudike, UmuahiaPMB 7006Nigeria
- College of Agriculture and Life SciencesCornell University215 Garden AvenueIthacaNY14853USA
| | - Hale Tufan
- College of Agriculture and Life SciencesCornell University215 Garden AvenueIthacaNY14853USA
| | - Peter Kulakow
- International Institute of Tropical AgricultureIbadanPMB 5320Nigeria
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20
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Mbanjo EGN, Rabbi IY, Ferguson ME, Kayondo SI, Eng NH, Tripathi L, Kulakow P, Egesi C. Technological Innovations for Improving Cassava Production in Sub-Saharan Africa. Front Genet 2021; 11:623736. [PMID: 33552138 PMCID: PMC7859516 DOI: 10.3389/fgene.2020.623736] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production.
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Affiliation(s)
| | | | | | | | - Ng Hwa Eng
- CGIAR Excellence in Breeding Platform, El Batan, Mexico
| | - Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- National Root Crops Research Institute, Umudike, Nigeria
- Department of Global Development, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
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21
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Akinsanya AK, Afolami SO, Kulakow P, Coyne D. The root-knot nematode, Meloidogyne incognita, profoundly affects the production of popular biofortified cassava cultivars. NEMATOLOGY 2020. [DOI: 10.1163/15685411-00003331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Despite being the single largest cassava-producing country, yields in Nigeria remain consistently poor and among the lowest. Regionally, yields are also particularly low across Africa. Pests and pathogens, including plant-parasitic nematodes, play an important role in this current yield deficit. African countries are not only faced with the problem of food security but also that of nutritional deficiency, due to limited micronutrients in the diet. In this study, six biofortified cultivars were evaluated for their response to inoculation with approximately 30 000 root-knot nematode (Meloidogyne incognita) eggs in 30 l pots in Nigeria. All cassava cultivars proved highly susceptible to M. incognita infection after 6 months, with nematode reproduction factor ranging from 7.0 to 44.8. Galling was common on feeder roots and gall index scores were recorded between 4 to 5 (on a scale of 1-5 where 5 ⩽ 100 galls). Meloidogyne incognita infection significantly reduced plant height, stem girth, fresh plant mass, fresh storage root number and storage root weight. Percentage yield loss of between 41.8-88.4% was recorded in M. incognita-infected plants compared with non-infected controls. Although M. incognita reduced storage root weight, it did not necessarily affect the nutritional quality (total carotenoid) or dry weight percentage of the biofortified cassava cultivars. Total carotenoid and dry weight contents of the control cultivar were similar to some of the biofortified cultivars. The high susceptibility of the biofortified cassava cultivars to M. incognita infection indicates that substantial yield losses are likely being experienced by farmers, as this nematode pest is prevalent across sub-Saharan Africa and the tropics.
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Affiliation(s)
- Aminat Korede Akinsanya
- 1Department of Crop Protection, Federal University of Agriculture, P.M.B. 2240, Abeokuta, Ogun State, Nigeria
- 2International Institute of Tropical Agriculture (IITA), Headquarters and West Africa Hub, P.M.B. 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria
| | - Steve Olaoluwa Afolami
- 1Department of Crop Protection, Federal University of Agriculture, P.M.B. 2240, Abeokuta, Ogun State, Nigeria
| | - Peter Kulakow
- 2International Institute of Tropical Agriculture (IITA), Headquarters and West Africa Hub, P.M.B. 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria
| | - Danny Coyne
- 2International Institute of Tropical Agriculture (IITA), Headquarters and West Africa Hub, P.M.B. 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria
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22
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Akinsanya A, Afolami S, Kulakow P, Parkes E, Coyne D. Popular Biofortified Cassava Cultivars Are Heavily Impacted by Plant Parasitic Nematodes, Especially Meloidogyne Spp. Plants (Basel) 2020; 9:E802. [PMID: 32604898 PMCID: PMC7356864 DOI: 10.3390/plants9060802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/01/2020] [Accepted: 06/23/2020] [Indexed: 11/16/2022]
Abstract
The development of new biofortified cassava cultivars, with higher micronutrient contents, offers great potential to enhance food and nutrition security prospects. Among the various constraints affecting cassava production are plant parasitic nematodes (PPN), especially root-knot nematodes. In this study, six popular biofortified cultivars were field-evaluated for their response to PPN in Nigeria. A field naturally infested with a diversity of PPN but dominated by root-knot nematodes was used. Application of the nematicide carbofuran significantly reduced PPN densities, and at harvest, no root galling damage was observed, compared with untreated plots, which had heavy galling damage. Plant height, stem girth, plant weight, marketable storage root number and weight were significantly lower for most cultivars in untreated plots. Percentage yield losses in the range of 21.3-63.7% were recorded from two separate trials conducted for 12 months each. Lower total carotenoid and dry matter contents were associated with higher PPN densities in some biofortified cultivars, resulting in a loss of as much as 63% of total carotenoid and 52% of dry matter contents. The number and weight of rotted storage roots were significantly greater in untreated plots across cultivars, reducing in-field and post-harvest storability. This study demonstrates that natural field populations of PPN can substantially affect yield, quality and nutritional value of released biofortified cassava cultivars.
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Affiliation(s)
- Aminat Akinsanya
- Department of Crop Protection, Federal University of Agriculture, P.M.B. 2240, Abeokuta 110001, Ogun State, Nigeria; or
- International Institute of Tropical Agriculture, P.M.B. 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria; (P.K.); (E.P.); (D.C.)
| | - Steve Afolami
- Department of Crop Protection, Federal University of Agriculture, P.M.B. 2240, Abeokuta 110001, Ogun State, Nigeria; or
| | - Peter Kulakow
- International Institute of Tropical Agriculture, P.M.B. 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria; (P.K.); (E.P.); (D.C.)
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture, P.M.B. 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria; (P.K.); (E.P.); (D.C.)
| | - Danny Coyne
- International Institute of Tropical Agriculture, P.M.B. 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria; (P.K.); (E.P.); (D.C.)
- Nematology Research Unit, Department of Biology, Ghent University, 9000 Gent, Belgium
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23
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Yonis BO, Pino Del Carpio D, Wolfe M, Jannink JL, Kulakow P, Rabbi I. Improving root characterisation for genomic prediction in cassava. Sci Rep 2020; 10:8003. [PMID: 32409788 PMCID: PMC7224197 DOI: 10.1038/s41598-020-64963-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 04/23/2020] [Indexed: 11/08/2022] Open
Abstract
Cassava is cultivated due to its drought tolerance and high carbohydrate-containing storage roots. The lack of uniformity and irregular shape of storage roots poses constraints on harvesting and post-harvest processing. Here, we phenotyped the Genetic gain and offspring (C1) populations from the International Institute of Tropical Agriculture (IITA) breeding program using image analysis of storage root photographs taken in the field. In the genome-wide association analysis (GWAS), we detected for most shape and size-related traits, QTL on chromosomes 1 and 12. In a previous study, we found the QTL on chromosome 12 to be associated with cassava mosaic disease (CMD) resistance. Because the root uniformity is important for breeding, we calculated the standard deviation (SD) of individual root measurements per clone. With SD measurements we identified new significant QTL for Perimeter, Feret and Aspect Ratio on chromosomes 6, 9 and 16. Predictive accuracies of root size and shape image-extracted traits were mostly higher than yield trait prediction accuracies. This study aimed to evaluate the feasibility of the image phenotyping protocol and assess GWAS and genomic prediction for size and shape image-extracted traits. The methodology described and the results are promising and open up the opportunity to apply high-throughput methods in cassava.
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Affiliation(s)
| | - Dunia Pino Del Carpio
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14850, USA
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBioscience, Bundoora, Australia
| | - Marnin Wolfe
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Jean-Luc Jannink
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14850, USA
- US Department of Agriculture - Agricultural Research Service (USDA-ARS), Ithaca, NY, USA
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria.
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24
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Ezenwaka L, Rabbi I, Onyeka J, Kulakow P, Egesi C. Identification of additional /novel QTL associated with resistance to cassava green mite in a biparental mapping population. PLoS One 2020; 15:e0231008. [PMID: 32240258 PMCID: PMC7117712 DOI: 10.1371/journal.pone.0231008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/13/2020] [Indexed: 11/19/2022] Open
Abstract
Cassava green mite [CGM, Mononychellus tanajoa (Bondar)] is the most destructive dry-season pest in most cassava production areas. The pest is responsible for cassava fresh root yield losses of over 80%. Deployment of CGM resistant cultivars is the most cost-effective and sustainable approach of alleviating such production losses. The purposes of this study were to validate the stability of CGM resistance genes found in previously published results, to identify new genes for CGM resistance in bi-parental mapping population and estimate the heritability of the trait. A total of 109 F1 progeny derived from a cross between CGM resistant parent, TMEB778 and a very susceptible parent, TMEB419 were evaluated under CGM hotspot areas in Nigeria for two cropping seasons. A total of 42,204 SNP markers with MAF ≥ 0.05 were used for single-marker analysis. The most significant QTL (S12_7962234) was identified on the left arm on chromosome 12 which explained high phenotypic variance and harboured significant single nucleotide polymorphism (SNP) markers conferring resistance to CGM and leaf pubescence (LP). Colocalization of the most significant SNP associated with resistance to CGM and LP on chromosome 12 is possibly an indication of a beneficial pleiotropic effect or are physically linked. These significant SNPs markers were intersected with the gene annotations and 33 unique genes were identified within SNPs at 4 - 8MB on chromosome 12. Among these genes, nine novel candidate genes namely; Manes.12077600, Manes.12G086200, Manes.12G061200, Manes.12G083100, Manes.12G082000, Manes.12G094100, Manes.12G075600, Manes.12G091400 and Manes.12G069300 highly expressed direct link to cassava green mite resistance. Pyramiding the new QTL/genes identified on chromosome 12 in this study with previously discovered loci, such on chromosome 8, will facilitate breeding varieties that are highly resistant CGM.
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Affiliation(s)
- Lydia Ezenwaka
- National Root Crops Research Institute, NRCRI, Umudike, Nigeria
| | - Ismail Rabbi
- International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Joseph Onyeka
- National Root Crops Research Institute, NRCRI, Umudike, Nigeria
| | - Peter Kulakow
- International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Chiedozie Egesi
- National Root Crops Research Institute, NRCRI, Umudike, Nigeria
- International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States of America
- * E-mail:
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25
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Karim KY, Ifie B, Dzidzienyo D, Danquah EY, Blay ET, Whyte JBA, Kulakow P, Rabbi I, Parkes E, Omoigui L, Norman PE, Iluebbey P. Genetic characterization of cassava ( Manihot esculenta Crantz) genotypes using agro-morphological and single nucleotide polymorphism markers. Physiol Mol Biol Plants 2020; 26:317-330. [PMID: 32158137 PMCID: PMC7036393 DOI: 10.1007/s12298-019-00740-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/15/2019] [Accepted: 11/24/2019] [Indexed: 06/01/2023]
Abstract
Dearth of information on extent of genetic variability in cassava limits the genetic improvement of cassava genotypes in Sierra Leone. The aim of this study was to assess the genetic diversity and relationships within 102 cassava genotypes using agro-morphological and single nucleotide polymorphism markers. Morphological classification based on qualitative traits categorized the germplasm into five different groups, whereas the quantitative trait set had four groups. The SNP markers classified the germplasm into three main cluster groups. A total of seven principal components (PCs) in the qualitative and four PCs in the quantitative trait sets accounted for 79.03% and 72.30% of the total genetic variation, respectively. Significant and positive correlations were observed between average yield per plant and harvest index (r = 0.76***), number of storage roots per plant and harvest index (r = 0.33*), height at first branching and harvest index (0.26*), number of storage roots per plant and average yield per plant (r = 0.58*), height at first branching and average yield per plant (r = 0.24*), length of leaf lobe and petiole length (r = 0.38*), number of leaf lobe and petiole length (r = 0.31*), width of leaf lobe and length of leaf lobe (r = 0.36*), number of leaf lobe and length of leaf lobe (r = 0.43*), starch content and dry matter content (r = 0.99***), number of leaf lobe and root dry matter (r = 0.30*), number of leaf lobe and starch content (r = 0.28*), and height at first branching and plant height (r = 0.45**). Findings are useful for conservation, management, short term recommendation for release and genetic improvement of the crop.
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Affiliation(s)
- Kumba Y. Karim
- Sierra Leone Agricultural Research Institute, Tower Hill, Freetown, PMB 1313 Sierra Leone
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Beatrice Ifie
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Daniel Dzidzienyo
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Eric Y. Danquah
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Essie T. Blay
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Jim B. A. Whyte
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Lucky Omoigui
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Prince E. Norman
- Sierra Leone Agricultural Research Institute, Tower Hill, Freetown, PMB 1313 Sierra Leone
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Peter Iluebbey
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
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26
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Peprah BB, Parkes E, Manu-Aduening J, Kulakow P, van Biljon A, Labuschagne M. Genetic variability, stability and heritability for quality and yield characteristics in provitamin A cassava varieties. Euphytica 2020; 216:31. [PMID: 32055054 PMCID: PMC6988135 DOI: 10.1007/s10681-020-2562-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/11/2020] [Indexed: 05/20/2023]
Abstract
Cassava is widely consumed in many areas of Africa, including Ghana, and is a major part of most household diets. These areas are characterized by rampant malnutrition, because the tuberous roots are low in nutritional value. Provitamin A biofortified cassava varieties have been developed by the International Institute for Tropical Agriculture, but adoption of these varieties in Ghana will largely depend on their agronomic performance, including fresh root yield, dry matter content, resistance to major pests and diseases, mealiness, starch content and the stability of these traits. Eight provitamin A varieties with two white checks were planted in three environments for two seasons to determine stability and variability among the varieties for important traits. There were significant variations in performance between varieties and between environments for cassava mosaic disease, root number, fresh root yield and starch content. High broad-sense heritability and genetic advance were observed in all traits, except for storage root number, and could be exploited through improvement programs. This study identified the best performing enhanced provitamin A varieties for traits that are key drivers of variety adoption in Ghana. In view of this, some varieties can be recommended for varietal release after on-farm testing. The study also showed the possibility of tapping heterosis after careful selection of parents.
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Affiliation(s)
- Bright Boakye Peprah
- CSIR-Crops Research Institute, Kumasi, Ghana
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Angeline van Biljon
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Maryke Labuschagne
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
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27
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Wolfe MD, Bauchet GJ, Chan AW, Lozano R, Ramu P, Egesi C, Kawuki R, Kulakow P, Rabbi I, Jannink JL. Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection. Genetics 2019; 213:1237-1253. [PMID: 31624088 PMCID: PMC6893375 DOI: 10.1534/genetics.119.302757] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Introgression of alleles from wild relatives has often been adaptive in plant breeding. However, the significance of historical hybridization events in modern breeding is often not clear. Cassava (Manihot esculenta) is among the most important staple foods in the world, sustaining hundreds of millions of people in the tropics, especially in sub-Saharan Africa. Widespread genotyping makes cassava a model for clonally propagated root and tuber crops in the developing world, and provides an opportunity to study the modern benefits and consequences of historical introgression. We detected large introgressed Manihot glaziovii genome-segments in a collection of 2742 modern cassava landraces and elite germplasm, the legacy of a 1930s era breeding to combat disease epidemics. African landraces and improved varieties were, on average, 3.8% (max 13.6%) introgressed. Introgressions accounted for a significant (mean 20%, max 56%) portion of the heritability of tested traits. M. glaziovii alleles on the distal 10 Mb of chr. 1 increased dry matter and root number. On chr. 4, introgressions in a 20 Mb region improved harvest index and brown streak disease tolerance. We observed the introgression frequency on chr. 1 double over three cycles of selection, and that later stage trials selectively excluded homozygotes from consideration as varieties. This indicates a heterozygous advantage of introgressions. However, we also found that maintaining large recombination-suppressed introgressions in the heterozygous state allowed the accumulation of deleterious mutations. We conclude that targeted recombination of introgressions would increase the efficiency of cassava breeding by allowing simultaneous fixation of beneficial alleles and purging of genetic load.
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Affiliation(s)
- Marnin D Wolfe
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
| | | | - Ariel W Chan
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
| | - Roberto Lozano
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
| | - Punna Ramu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850
| | - Chiedozie Egesi
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14850
- National Root Crops Research Institute (NRCRI), Umudike, Umuahia, 440221, Nigeria
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Robert Kawuki
- National Root Crops Resources Research Institute, Namulonge, Uganda
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Jean-Luc Jannink
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
- United States Department of Agriculture - Agriculture Research Service, Ithaca, New York 14850
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28
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Abstract
Although numerous studies of diversity have been conducted in cassava, there is no comprehensive assessment of global genetic diversity. Here we draw on previous studies and breeders' knowledge to select diversity sets from the International Institute of Tropical Agriculture (IITA) and the International Center for Tropical Agriculture (CIAT) genebanks and breeders' germplasm, as well as elite germplasm and landraces from eastern, southern and central (ESC) Africa to make a global assessment of diversity in cassava, using a SNP based GoldenGate (Illumina Inc.) assay. A synthesis of results from genetic distance and ADMIXTURE analysis essentially revealed four populations (i) South American germplasm characterised by relatively higher genetic diversity with hypothetical ancestral founder genotypes from Brazil, (ii) a smaller group of African introduction germplasm which is more distantly related to all other germplasm, (iii) West Africa germplasm dominated by IITA breeding lines, containing sources of cassava mosaic disease resistance, and IITA genebank accessions from West Africa, both characterised by slightly lower diversity, and (iv) a less cohesive group of African germplasm, termed 'Other', with moderate levels of diversity and a majority of germplasm from ESC Africa. This study highlights opportunities for heterosis breeding, purging of duplicates in genebanks and the need for conservation of ESC Africa landraces.
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Affiliation(s)
- Morag E. Ferguson
- International Institute of Tropical Agriculture, Nairobi, Kenya
- * E-mail:
| | - Trushar Shah
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Hernan Ceballos
- International Center for Tropical Agriculture, Cali, Colombia
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29
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Omidiran AT, Sobukola OP, Sanni SA, Sanni LO, Adebowale AA, Shajobi AO, Kulakow P. Evaluation of some quality parameters of cassava starch and soy protein isolate matrices during deep fat frying in soybean oil. Food Sci Nutr 2019; 7:656-666. [PMID: 30847144 PMCID: PMC6392818 DOI: 10.1002/fsn3.904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/25/2018] [Accepted: 11/14/2018] [Indexed: 11/17/2022] Open
Abstract
Snack industry is recently focused on the production of snacks with minimal oil content and enhanced quality attributes which prompted the need to study the changes in snack matrices produced from cassava starch processed from three varieties of cassava roots (TMS-950289, TME-419, and TMS-30572) and soy protein isolate blends fried in soybean oil. Effect of frying temperature (170-180°C), frying time (2-4 min), soy protein isolate inclusion level (5%-15%) on proximate composition, color changes, expansion, texture, and sensory attributes of the snacks was investigated. Optimization of process variables was carried out based on a factorial design (2 level by 3 factor) in the Design Expert version 6.0.8, and models were generated showing the relationship between the independent variables and the responses. The desired goal for each constraint (processing conditions) was kept within 170-180°C for 2-4 min, while all responses, except chewiness, expansion, yellowness, and protein, were set at minimum. Evaluation of sensory attributes of the optimized sample was carried out to determine its level of desirability. The optimized frying conditions for matrices produced from starches of TMS-950289 are 170°C/4 min/5% SPI with desirability value of 0.507; from TME-419 are 180°C/2 min/5% SPI with desirability value of 0.475 while for those from TMS-30572 are 170°C/4 min/15% SPI with desirability value of 0.459. At higher SPI level, the protein content was high at 170°C. At 4 min frying time for all the varieties, the moisture content reduces. The most desired optimized fried snack produced from starch of TMS-30572 (containing 15% SPI) had higher crispness and lower oil content than other optimized fried snacks.
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Affiliation(s)
- Adebukola T. Omidiran
- Department of Food Science and TechnologyFederal University of AgricultureAbeokutaNigeria
| | - Olajide P. Sobukola
- Department of Food Science and TechnologyFederal University of AgricultureAbeokutaNigeria
| | - Silifat A. Sanni
- Department of Nutrition and DieteticsFederal University of AgricultureAbeokutaNigeria
| | - Lateef O. Sanni
- Department of Food Science and TechnologyFederal University of AgricultureAbeokutaNigeria
| | | | - Adebola O. Shajobi
- Department of Food Science and TechnologyFederal University of AgricultureAbeokutaNigeria
| | - Peter Kulakow
- Cassava Breeding UnitInternational Institute of Tropical AgricultureIbadanNigeria
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30
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Olaosebikan O, Abdulrazaq B, Owoade D, Ogunade A, Aina O, Ilona P, Muheebwa A, Teeken B, Iluebbey P, Kulakow P, Bakare M, Parkes E. Gender-based constraints affecting biofortified cassava production, processing and marketing among men and women adopters in Oyo and Benue States, Nigeria. Physiol Mol Plant Pathol 2019; 105:17-27. [PMID: 31007372 PMCID: PMC6472612 DOI: 10.1016/j.pmpp.2018.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 10/29/2018] [Accepted: 11/25/2018] [Indexed: 06/09/2023]
Abstract
This study identified gender-based constraints affecting the production, processing and marketing of biofortified cassava in two states in Nigeria, using a mixed methods approach. The study identified major differences between the two study sites (Benue and Oyo). The scale of production of biofortified cassava is higher in Oyo state among adult men because of their active involvement and collaboration with research institutes within the state and the ease of transporting products to Lagos State for designated diverse markets. However, in Benue state more adult and young women are engaged in cultivation, processing and marketing business to meet up with the increased demand due to higher consumer acceptance in this region. Gender analysis revealed that lack of access to hired-labour restricted the scale of production among women in especially Oyo state. Low product price and high price of processing equipment, poor market infrastructure and middle men exploitation were constraints significantly more mentioned by women in general. Majorly, the men identified limited processing facilities/equipment as the most important constraint affecting the demand of biofortified cassava roots, while generally women were more constrained by the shortage of basic amenities and trainings that hindered their processing efficiency. The study proposes integration of gender-responsive strategies to further enhance the delivery of biofortified cassava products in Nigeria.
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Affiliation(s)
- Olamide Olaosebikan
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Gender-Responsive Researchers Equipped for Agricultural Transformation (GREAT) RTB Fellows, Nigeria
| | - Bello Abdulrazaq
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Gender-Responsive Researchers Equipped for Agricultural Transformation (GREAT) RTB Fellows, Nigeria
| | - Durodola Owoade
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Gender-Responsive Researchers Equipped for Agricultural Transformation (GREAT) RTB Fellows, Nigeria
| | - Adedayo Ogunade
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Olufemi Aina
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | | | - Béla Teeken
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Peter Iluebbey
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Moshood Bakare
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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31
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Ozimati A, Kawuki R, Esuma W, Kayondo IS, Wolfe M, Lozano R, Rabbi I, Kulakow P, Jannink JL. Training Population Optimization for Prediction of Cassava Brown Streak Disease Resistance in West African Clones. G3 (Bethesda) 2018; 8:3903-3913. [PMID: 30373913 PMCID: PMC6288821 DOI: 10.1534/g3.118.200710] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/13/2018] [Indexed: 02/06/2023]
Abstract
Cassava production in the central, southern and eastern parts of Africa is under threat by cassava brown streak virus (CBSV). Yield losses of up to 100% occur in cases of severe infections of edible roots. Easy illegal movement of planting materials across African countries, and long-range movement of the virus vector (Bemisia tabaci) may facilitate spread of CBSV to West Africa. Thus, effort to pre-emptively breed for CBSD resistance in W. Africa is critical. Genomic selection (GS) has become the main approach for cassava breeding, as costs of genotyping per sample have declined. Using phenotypic and genotypic data (genotyping-by-sequencing), followed by imputation to whole genome sequence (WGS) for 922 clones from National Crops Resources Research Institute, Namulonge, Uganda as a training population (TP), we predicted CBSD symptoms for 35 genotyped W. African clones, evaluated in Uganda. The highest prediction accuracy (r = 0.44) was observed for cassava brown streak disease severity scored at three months (CBSD3s) in the W. African clones using WGS-imputed markers. Optimized TPs gave higher prediction accuracies for CBSD3s and CBSD6s than random TPs of the same size. Inclusion of CBSD QTL chromosome markers as kernels, increased prediction accuracies for CBSD3s and CBSD6s. Similarly, WGS imputation of markers increased prediction accuracies for CBSD3s and for cassava brown streak disease root severity (CBSDRs), but not for CBSD6s. Based on these results we recommend TP optimization, inclusion of CBSD QTL markers in genomic prediction models, and the use of high-density (WGS-imputed) markers for CBSD predictions across population.
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Affiliation(s)
- Alfred Ozimati
- National Crops Resources Research Institute (NaCRRI), P.O. Box, 7084 Kampala, Uganda
- School of Integrative Plant Science, Plant breeding and Genetics Section, Cornell University, Ithaca, New York
| | - Robert Kawuki
- National Crops Resources Research Institute (NaCRRI), P.O. Box, 7084 Kampala, Uganda
| | - Williams Esuma
- National Crops Resources Research Institute (NaCRRI), P.O. Box, 7084 Kampala, Uganda
| | - Ismail Siraj Kayondo
- National Crops Resources Research Institute (NaCRRI), P.O. Box, 7084 Kampala, Uganda
| | - Marnin Wolfe
- School of Integrative Plant Science, Plant breeding and Genetics Section, Cornell University, Ithaca, New York
| | - Roberto Lozano
- School of Integrative Plant Science, Plant breeding and Genetics Section, Cornell University, Ithaca, New York
| | - Ismail Rabbi
- International Institute for Tropical Agriculture (IITA), Ibadan, Oyo, Nigeria
| | - Peter Kulakow
- International Institute for Tropical Agriculture (IITA), Ibadan, Oyo, Nigeria
| | - Jean-Luc Jannink
- School of Integrative Plant Science, Plant breeding and Genetics Section, Cornell University, Ithaca, New York
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R.W. Holley Center for Agriculture and Health, Ithaca 14853, NY
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32
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Abioye V, Adeyemi I, Akinwande B, Kulakow P, Maziya-Dixon B. Effect of autoclaving on the formation of resistant starch from two Nigeria Cassava (Manihot esculenta) varieties. Food Res 2018. [DOI: 10.26656/fr.2017.2(5).205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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33
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Elias AA, Rabbi I, Kulakow P, Jannink JL. Improving Genomic Prediction in Cassava Field Experiments by Accounting for Interplot Competition. G3 (Bethesda) 2018; 8:933-944. [PMID: 29358232 PMCID: PMC5844313 DOI: 10.1534/g3.117.300354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/09/2018] [Indexed: 11/24/2022]
Abstract
Plants competing for available resources is an unavoidable phenomenon in a field. We conducted studies in cassava (Manihot esculenta Crantz) in order to understand the pattern of this competition. Taking into account the competitive ability of genotypes while selecting parents for breeding advancement or commercialization can be very useful. We assumed that competition could occur at two levels: (i) the genotypic level, which we call interclonal, and (ii) the plot level irrespective of the type of genotype, which we call interplot competition or competition error. Modification in incidence matrices was applied in order to relate neighboring genotype/plot to the performance of a target genotype/plot with respect to its competitive ability. This was added into a genomic selection (GS) model to simultaneously predict the direct and competitive ability of a genotype. Predictability of the models was tested through a 10-fold cross-validation method repeated five times. The best model was chosen as the one with the lowest prediction root mean squared error (pRMSE) compared to that of the base model having no competitive component. Results from our real data studies indicated that <10% increase in accuracy was achieved with GS-interclonal competition model, but this value reached up to 25% with a GS-competition error model. We also found that the competitive influence of a cassava clone is not just limited to the adjacent neighbors but spreads beyond them. Through simulations, we found that a 26% increase of accuracy in estimating trait genotypic effect can be achieved even in the presence of high competitive variance.
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Affiliation(s)
- Ani A Elias
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853
| | - Ismail Rabbi
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria and
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria and
| | - Jean-Luc Jannink
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853
- United States Department of Agriculture-Agricultural Research Station (USDA-ARS), Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853-2901
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34
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Okeke UG, Akdemir D, Rabbi I, Kulakow P, Jannink JL. Regional Heritability Mapping Provides Insights into Dry Matter Content in African White and Yellow Cassava Populations. Plant Genome 2018; 11:10.3835/plantgenome2017.06.0050. [PMID: 29505634 PMCID: PMC7822058 DOI: 10.3835/plantgenome2017.06.0050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 06/20/2017] [Indexed: 05/21/2023]
Abstract
The HarvestPlus program for cassava ( Crantz) fortifies cassava with β-carotene by breeding for carotene-rich tubers (yellow cassava). However, a negative correlation between yellowness and dry matter (DM) content has been identified. We investigated the genetic control of DM in white and yellow cassava. We used regional heritability mapping (RHM) to associate DM with genomic segments in both subpopulations. Significant segments were subjected to candidate gene analysis and candidates were validated with prediction accuracies. The RHM procedure was validated via a simulation approach and revealed significant hits for white cassava on chromosomes 1, 4, 5, 10, 17, and 18, whereas hits for the yellow were on chromosome 1. Candidate gene analysis revealed genes in the carbohydrate biosynthesis pathway including plant serine-threonine protein kinases (SnRKs), UDP (uridine diphosphate)-glycosyltransferases, UDP-sugar transporters, invertases, pectinases, and regulons. Validation using 1252 unique identifiers from the SnRK gene family genome-wide recovered 50% of the predictive accuracy of whole-genome single nucleotide polymorphisms for DM, whereas validation using 53 likely genes (extracted from the literature) from significant segments recovered 32%. Genes including an acid invertase, a neutral or alkaline invertase, and a glucose-6-phosphate isomerase were validated on the basis of an a priori list for the cassava starch pathway, and also a fructose-biphosphate aldolase from the Calvin cycle pathway. The power of the RHM procedure was estimated as 47% when the causal quantitative trait loci generated 10% of the phenotypic variance (sample size = 451). Cassava DM genetics are complex and RHM may be useful for complex traits.
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Affiliation(s)
- Uche Godfrey Okeke
- Section of Plant Breeding and Genetics, School of Integrative
Plant Sci., College of Agriculture and Life Sci., Cornell Univ., 14853, Ithaca,
NY
| | - Deniz Akdemir
- Section of Plant Breeding and Genetics, School of Integrative
Plant Sci., College of Agriculture and Life Sci., Cornell Univ., 14853, Ithaca,
NY
- current address, Statgen Consulting, Ithaca, NY 14850
| | | | | | - Jean-Luc Jannink
- Section of Plant Breeding and Genetics, School of Integrative
Plant Sci., College of Agriculture and Life Sci., Cornell Univ., 14853, Ithaca,
NY
- USDAARS, Robert W. Holley Centre for Agriculture and Health, Tower
Road, Ithaca, NY 14853
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35
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Teeken B, Olaosebikan O, Haleegoah J, Oladejo E, Madu T, Bello A, Parkes E, Egesi C, Kulakow P, Kirscht H, Tufan HA. Cassava Trait Preferences of Men and Women Farmers in Nigeria: Implications for Breeding. Econ Bot 2018; 72:263-277. [PMID: 30573920 PMCID: PMC6267705 DOI: 10.1007/s12231-018-9421-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/18/2018] [Indexed: 05/21/2023]
Abstract
Nigeria is the world's largest cassava producer, hosting a diverse array of cassava farmers and processors. Cassava breeding programs prioritize "common denominator" traits in setting breeding agendas, to impact the largest possible number of people through improved varieties. This approach has been successful, but cassava adoption rates are less than expected, with room for improvement by integrating traits in demand by farmers and processors. This paper aims to inform breeding priority setting, by examining trait and varietal preferences of men and women cassava farmer/processors. Men and women in eight communities in Southwest and Southeast Nigeria were consulted using mixed methods. Women and men had significantly different patterns of cassava use in the Southwest. Fifty-five variety names were recorded from the communities demonstrating high genetic diversity maintained by growers, especially in the Southeast. High yield, early maturity, and root size were most important traits across both regions, while traits women and men preferred followed gender roles: women prioritized product quality/cooking traits, while men placed higher priority on agronomic traits. Trait preference patterns differed significantly between the Southeast and Southwest, and showed differentiation based on gender. Patterns of access to stem sources were determined more by region and religion than gender.
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Affiliation(s)
- Béla Teeken
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Joyce Haleegoah
- Council on Science and Industrial Research-Crops Research Institute (CSIR-CRI), Accra, Ghana
| | - Elizabeth Oladejo
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Tessy Madu
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - Abolore Bello
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- Cornell University, Ithaca, New York USA
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Holger Kirscht
- Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ), Bonn, Germany
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36
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Rabbi IY, Udoh LI, Wolfe M, Parkes EY, Gedil MA, Dixon A, Ramu P, Jannink JL, Kulakow P. Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content. Plant Genome 2017; 10:10.3835/plantgenome2016.09.0094. [PMID: 29293815 PMCID: PMC7822061 DOI: 10.3835/plantgenome2016.09.0094] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 06/12/2017] [Indexed: 05/19/2023]
Abstract
Cassava is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Primary selection objectives in cassava breeding include dry matter content and micronutrient density, particularly provitamin A carotenoids. These traits are negatively correlated in the African germplasm. This study aimed at identifying genetic markers associated with these traits and uncovering whether linkage and/or pleiotropy were responsible for observed negative correlation. A genome-wide association mapping using 672 clones genotyped at 72,279 single nucleotide polymorphism (SNP) loci was performed. Root yellowness was used indirectly to assess variation in carotenoid content. Two major loci for root yellowness were identified on chromosome 1 at positions 24.1 and 30.5 Mbp. A single locus for dry matter content that colocated with the 24.1 Mbp peak for carotenoids was identified. Haplotypes at these loci explained 70 and 37% of the phenotypic variability for root yellowness and dry matter content, respectively. Evidence of megabase-scale linkage disequilibrium (LD) around the major loci of the two traits and detection of the major dry matter locus in independent analysis for the white- and yellow-root subpopulations suggests that physical linkage rather that pleiotropy is more likely to be the cause of the negative correlation between the target traits. Moreover, candidate genes for carotenoid () and starch biosynthesis ( and ) occurred in the vicinity of the identified locus at 24.1 Mbp. These findings elucidate the genetic architecture of carotenoids and dry matter in cassava and provide an opportunity to accelerate breeding of these traits.
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Affiliation(s)
- Ismail Y. Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
- Corresponding author ()
| | - Lovina I. Udoh
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Marnin Wolfe
- Dep. of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY 14853
| | - Elizabeth Y. Parkes
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Melaku A. Gedil
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Alfred Dixon
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Punna Ramu
- Institute of Genomic Diversity, Cornell Univ., Ithaca, NY 14853
| | - Jean-Luc Jannink
- Dep. of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY 14853
- USDA-ARS, R.W. Holley Center for Agriculture and Health, Ithaca, NY 14853
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
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37
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Wolfe MD, Carpio DPD, Alabi O, Ezenwaka LC, Ikeogu UN, Kayondo IS, Lozano R, Okeke UG, Ozimati AA, Williams E, Egesi C, Kawuki RS, Kulakow P, Rabbi IY, Jannink JL. Prospects for Genomic Selection in Cassava Breeding. Plant Genome 2017; 10:10.3835/plantgenome2017.03.0015. [PMID: 29293806 PMCID: PMC7822052 DOI: 10.3835/plantgenome2017.03.0015] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Cassava ( Crantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) has been implemented at three breeding institutions in Africa to reduce cycle times. Initial studies provided promising estimates of predictive abilities. Here, we expand on previous analyses by assessing the accuracy of seven prediction models for seven traits in three prediction scenarios: cross-validation within populations, cross-population prediction and cross-generation prediction. We also evaluated the impact of increasing the training population (TP) size by phenotyping progenies selected either at random or with a genetic algorithm. Cross-validation results were mostly consistent across programs, with nonadditive models predicting of 10% better on average. Cross-population accuracy was generally low (mean = 0.18) but prediction of cassava mosaic disease increased up to 57% in one Nigerian population when data from another related population were combined. Accuracy across generations was poorer than within-generation accuracy, as expected, but accuracy for dry matter content and mosaic disease severity should be sufficient for rapid-cycling GS. Selection of a prediction model made some difference across generations, but increasing TP size was more important. With a genetic algorithm, selection of one-third of progeny could achieve an accuracy equivalent to phenotyping all progeny. We are in the early stages of GS for this crop but the results are promising for some traits. General guidelines that are emerging are that TPs need to continue to grow but phenotyping can be done on a cleverly selected subset of individuals, reducing the overall phenotyping burden.
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Affiliation(s)
- Marnin D. Wolfe
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- Corresponding authors (, )
| | - Dunia Pino Del Carpio
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- Corresponding authors (, )
| | - Olumide Alabi
- International Inst. for Tropical Agriculture, Ibadan, Oyo, Nigeria
| | | | - Ugochukwu N. Ikeogu
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- National Root Crops Research Inst., Umudike, Umuahia, Nigeria
| | | | - Roberto Lozano
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
| | - Uche G. Okeke
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- International Inst. for Tropical Agriculture, Ibadan, Oyo, Nigeria
| | - Alfred A. Ozimati
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- National Crops Resources Research Inst., Namulonge, Uganda
| | - Esuma Williams
- National Crops Resources Research Inst., Namulonge, Uganda
| | - Chiedozie Egesi
- International Inst. for Tropical Agriculture, Ibadan, Oyo, Nigeria
- National Root Crops Research Inst., Umudike, Umuahia, Nigeria
- International Programs, College of Agriculture and Life Sciences, Cornell Univ., Ithaca, NY
| | | | - Peter Kulakow
- International Inst. for Tropical Agriculture, Ibadan, Oyo, Nigeria
| | - Ismail Y. Rabbi
- International Inst. for Tropical Agriculture, Ibadan, Oyo, Nigeria
| | - Jean-Luc Jannink
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- USDA-ARS, R.W. Holley Center for Agriculture and Health, Ithaca, NY
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38
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Wolfe MD, Rabbi IY, Egesi C, Hamblin M, Kawuki R, Kulakow P, Lozano R, Carpio DPD, Ramu P, Jannink JL. Genome-Wide Association and Prediction Reveals Genetic Architecture of Cassava Mosaic Disease Resistance and Prospects for Rapid Genetic Improvement. Plant Genome 2016; 9. [PMID: 27898832 DOI: 10.3835/plantgenome2015.11.0118] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
C ( Crantz) is a crucial, under-researched crop feeding millions worldwide, especially in Africa. Cassava mosaic disease (CMD) has plagued production in Africa for over a century. Biparental mapping studies suggest primarily a single major gene mediates resistance. To investigate this genetic architecture, we conducted the first genome-wide association mapping study in cassava with up to 6128 genotyping-by-sequenced African breeding lines and 42,113 reference genome-mapped single-nucleotide polymorphism (SNP) markers. We found a single region on chromosome 8 that accounts for 30 to 66% of genetic resistance in the African cassava germplasm. Thirteen additional regions with small effects were also identified. Further dissection of the major quantitative trait locus (QTL) on chromosome 8 revealed the presence of two possibly epistatic loci and/or multiple resistance alleles, which may account for the difference between moderate and strong disease resistances in the germplasm. Search of potential candidate genes in the major QTL region identified two peroxidases and one thioredoxin. Finally, we found genomic prediction accuracy of 0.53 to 0.58 suggesting that genomic selection (GS) will be effective both for improving resistance in breeding populations and identifying highly resistant clones as varieties.
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Bredeson JV, Lyons JB, Prochnik SE, Wu GA, Ha CM, Edsinger-Gonzales E, Grimwood J, Schmutz J, Rabbi IY, Egesi C, Nauluvula P, Lebot V, Ndunguru J, Mkamilo G, Bart RS, Setter TL, Gleadow RM, Kulakow P, Ferguson ME, Rounsley S, Rokhsar DS. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Nat Biotechnol 2016; 34:562-70. [PMID: 27088722 DOI: 10.1038/nbt.3535] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 03/10/2016] [Indexed: 11/09/2022]
Abstract
Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Simon E Prochnik
- United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA
| | - G Albert Wu
- United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA
| | - Cindy M Ha
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Eric Edsinger-Gonzales
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Jane Grimwood
- United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Jeremy Schmutz
- United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Ismail Y Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - Poasa Nauluvula
- Department of Agriculture, Ministry of Primary Industries, Koronivia Research Station, Fiji
| | - Vincent Lebot
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Port-Vila, Vanuatu
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam, Tanzania
| | - Geoffrey Mkamilo
- Naliendele Agricultural Research Institute (NARI), Mtwara, Tanzania
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Tim L Setter
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Roslyn M Gleadow
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Morag E Ferguson
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | | | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.,United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA.,Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
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Okike I, Samireddypalle A, Kaptoge L, Fauquet C, Atehnkeng J, Bandyopadhyay R, Kulakow P, Duncan A, Alabi T, Blummel M. Technical innovations for small-scale producers and households to process wet cassava peels into high quality animal feed ingredients and aflasafe™ substrate. ACTA ACUST UNITED AC 2015. [DOI: 10.3362/2046-1887.2015.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Iheanacho Okike
- Iheanacho Okike is Senior Agricultural Economist at the International Livestock Research Institute (ILRI), Ibadan, Nigeria
| | - Anandan Samireddypalle
- Anandan Samireddypalle is Livestock Nutritionist at the International Livestock Research Institute (ILRI), Ibadan, Nigeria
| | - Lawrence Kaptoge
- Lawrence Kaptoge is Process Engineer at the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Claude Fauquet
- Claude Fauquet is Director of the Global Cassava Partnership for the 21st Century (GCP21), CIAT, Cali, Colombia
| | - Joseph Atehnkeng
- Joseph Atehnkeng is Plant Pathologist at the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ranajit Bandyopadhyay
- Ranajit Bandyopadhyay is Senior Plant Pathologist at the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Peter Kulakow
- Peter Kulakow is Cassava Breeder/Geneticist at the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Alan Duncan
- Alan Duncan is Principal Livestock Scientist at ILRI, Addis Ababa, Ethiopia
| | - Tunrayo Alabi
- Tunrayo Alabi is GIS Specialist at the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Michael Blummel
- Michael Blümmel is Team Leader at ILRI, Addis Ababa, Ethiopia
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Tecle IY, Edwards JD, Menda N, Egesi C, Rabbi IY, Kulakow P, Kawuki R, Jannink JL, Mueller LA. solGS: a web-based tool for genomic selection. BMC Bioinformatics 2014; 15:398. [PMID: 25495537 PMCID: PMC4269960 DOI: 10.1186/s12859-014-0398-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 11/26/2014] [Indexed: 11/18/2022] Open
Abstract
Background Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide markers and statistical complexity, however, is a serious challenge in data management, analysis, and sharing. A bioinformatics infrastructure for data storage and access, and user-friendly web-based tool for analysis and sharing output is needed to make GS more practical for breeders. Results We have developed a web-based tool, called solGS, for predicting genomic estimated breeding values (GEBVs) of individuals, using a Ridge-Regression Best Linear Unbiased Predictor (RR-BLUP) model. It has an intuitive web-interface for selecting a training population for modeling and estimating genomic estimated breeding values of selection candidates. It estimates phenotypic correlation and heritability of traits and selection indices of individuals. Raw data is stored in a generic database schema, Chado Natural Diversity, co-developed by multiple database groups. Analysis output is graphically visualized and can be interactively explored online or downloaded in text format. An instance of its implementation can be accessed at the NEXTGEN Cassava breeding database, http://cassavabase.org/solgs. Conclusions solGS enables breeders to store raw data and estimate GEBVs of individuals online, in an intuitive and interactive workflow. It can be adapted to any breeding program. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0398-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isaak Y Tecle
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA.
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Khaitan S, Kalainesan S, Erickson L, Kulakow P, Martin S, Karthikeyan R, Hutchinson S, Davis L, Illangasekare T, Ng'oma C. Remediation of sites contaminated by oil refinery operations. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/ep.10083] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Banks MK, Kulakow P, Schwab AP, Chen Z, Rathbone K. Degradation of crude oil in the rhizosphere of Sorghum bicolor. Int J Phytoremediation 2003; 5:225-234. [PMID: 14750430 DOI: 10.1080/713779222] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Dissipation of petroleum contaminants in the rhizosphere is likely the result of enhanced microbial degradation. Plant roots may encourage rhizosphere microbial activity through exudation of nutrients and by providing channels for increased water flow and gas diffusion. Phytoremediation of crude oil in soil was examined in this study using carefully selected plant species monitored over specific plant growth stages. Four sorghum (Sorghum bicolor L.) genotypes with differing root characteristics and levels of exudation were established in a sandy loam soil contaminated with 2700 mg crude oil/kg soil. Soils were sampled at three stages of plant growth: five leaf, flowering, and maturity. All vegetated treatments were associated with higher remediation efficiency, resulting in significantly lower total petroleum hydrocarbon concentrations than unvegetated controls. A relationship between root exudation and bioremediation efficiency was not apparent for these genotypes, although the presence of all sorghum genotypes resulted in significant removal of crude oil from the impacted soil.
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Affiliation(s)
- M K Banks
- School of Civil Engineering, Purdue University, West Lafayette, IN 47907, USA
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Kulakow P, Jain S. Genetics of grain amaranths : 4. Variation and early generation response to selection in Amaranthus cruentus L. Theor Appl Genet 1987; 74:113-120. [PMID: 24241466 DOI: 10.1007/bf00290093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/1986] [Accepted: 11/27/1986] [Indexed: 05/28/2023]
Abstract
Two landrace populations of Amaranthus cruentus L. were crossed to generate F2 populations for quantitative genetic analyses of variation. Evidence for significant inbreeding depression in comparisons of F1 and F2generation means suggested some role of nonadditive gene action for days to first anthesis, leaf length, leaf width, petiole length, plant height, panicle length, and panicle weight. A pooled F2 population was subjected to bidirectional mass selection for time of first anthesis (two cycles) and leaf length (one cycle). Responses to selection were asymmetrical and the second cycle response for anthesis time was smaller than for the first cycle. Overall, selection gains were significant and gave estimates of heritability in the range of 0.35 to 0.66 for anthesis time and 0.08 to 0.19 for leaf length. This suggested a large additive term in the total genetic variance especially for anthesis time where early and late flowering selection lines diverged by 20.5 days.Correlations between the selected traits (anthesis time, leaf length) and single plant yield or yield components were also studied to evaluate correlated responses to selection. Selection for optimal flowering time in amaranth cultivation areas is very likely to result in rapid yield improvement.
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Affiliation(s)
- P Kulakow
- Department of Agronomy and Range Science, University of California, 95616, Davis, CA, USA
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