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da Conceicão LV, Cortes DFM, Klauser D, Robinson M, de Oliveira EJ. New protocol for rapid cassava multiplication in field conditions: a perspective on speed breeding. Front Plant Sci 2023; 14:1258101. [PMID: 37753503 PMCID: PMC10518405 DOI: 10.3389/fpls.2023.1258101] [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: 07/13/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023]
Abstract
Despite the economic and social importance, high-yielding cassava cultivars are only released after extensive research, mainly due to the low multiplication rate. This study aimed to assess the impact of using smaller-sized seed cuttings treated with agrochemicals (8MP) compared to the conventional planting size (16 cm) on genetic parameters, agronomic performance, and the ranking of cassava clones based on yield and growth attributes. The evaluation was carried out in clonal evaluation trial (CET), preliminary yield trial (PYT), and uniform yield trials (UYT). Additionally, a new selection scheme for cassava breeding programs was proposed. A total of 169 clones were evaluated, including 154 improved clones at different stages of selection and 15 local varieties used as checks. Field trials were conducted using both sizes of propagative material (8MP and 16 cm) in each phase of the breeding program. The data were analyzed using mixed models, considering the random effects of genotype and genotype-environment interaction (G×E) to determine variances and heritabilities. Bland-Altman concordance and correlation analysis of selection indices were employed to examine the consistency in the ranking of cassava clones using different seed cutting sizes. The distribution of variance components, heritabilities, means, and range of the 8MP and 16 cm trials in different phases of the cassava breeding program exhibited remarkable similarity, thereby enabling a comparative assessment of similar genetic effects. With a selection intensity of 30%, the concordance in clone ranking was 0.41, 0.57, and 0.85 in CET, PYT, and UYT trials, respectively, when comparing the selection based on 8MP and 16 cm trials. It is worth noting that the ranking of the top 15% remained largely unchanged. Based on the findings, proposed changes in the cassava selection scheme involve increasing the number of trials starting from the CET phase, early incorporation of G×E interaction, elimination of the PYT trial, reduction of the breeding cycle from 5 to 3 years, and a decrease in the time required for variety development from 11 to 9 years. These modifications are expected to lead to cost reduction and enhance the effectiveness of cassava breeding programs.
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Affiliation(s)
- Leila Verena da Conceicão
- Universidade Federal do Recôncavo da Bahia, Centro de Ciências Agrárias, Ambientais e Biológicas, Cruz das Almas, Bahia, Brazil
| | | | - Dominik Klauser
- Syngenta Foundation for Sustainable Agriculture, Basel, Switzerland
| | - Michael Robinson
- Syngenta Foundation for Sustainable Agriculture, Basel, Switzerland
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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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Ogbonna AC, Ramu P, Esuma W, Nandudu L, Morales N, Powell A, Kawuki R, Bauchet G, Jannink JL, Mueller LA. A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz). Sci Rep 2021; 11:23520. [PMID: 34876620 DOI: 10.1038/s41598-021-02794-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Cassava, a food security crop in Africa, is grown throughout the tropics and subtropics. Although cassava can provide high productivity in suboptimal conditions, the yield in Africa is substantially lower than in other geographies. The yield gap is attributable to many challenges faced by cassava in Africa, including susceptibility to diseases and poor soil conditions. In this study, we carried out 3’RNA sequencing on 150 accessions from the National Crops Resources Research Institute, Uganda for 5 tissue types, providing population-based transcriptomics resources to the research community in a web-based queryable cassava expression atlas. Differential expression and weighted gene co-expression network analysis were performed to detect 8820 significantly differentially expressed genes (DEGs), revealing similarity in expression patterns between tissue types and the clustering of detected DEGs into 18 gene modules. As a confirmation of data quality, differential expression and pathway analysis targeting cassava mosaic disease (CMD) identified 27 genes observed in the plant–pathogen interaction pathway, several previously identified CMD resistance genes, and two peroxidase family proteins different from the CMD2 gene. Present research work represents a novel resource towards understanding complex traits at expression and molecular levels for the development of resistant and high-yielding cassava varieties, as exemplified with CMD.
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Mafra GS, de Almeida Filho JE, do Amaral Junior AT, Maldonado C, Kamphorst SH, de Lima VJ, dos Santos Junior DR, Leite JT, Santos PHAD, de Oliveira Santos T, Bispo RB, de Oliveira UA, Pinto VB, Viana AP, Correa CCG, Ahmar S, Mora-poblete F. Regional Heritability Mapping of Quantitative Trait Loci Controlling Traits Related to Growth and Productivity in Popcorn (Zea mays L.). Plants 2021; 10:1845. [PMID: 34579378 PMCID: PMC8466968 DOI: 10.3390/plants10091845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/17/2022]
Abstract
The method of regional heritability mapping (RHM) has become an important tool in the identification of quantitative trait loci (QTLs) controlling traits of interest in plants. Here, RHM was first applied in a breeding population of popcorn, to identify the QTLs and candidate genes involved in grain yield, plant height, kernel popping expansion, and first ear height, as well as determining the heritability of each significant genomic region. The study population consisted of 98 S1 families derived from the 9th recurrent selection cycle (C-9) of the open-pollinated variety UENF-14, which were genetically evaluated in two environments (ENV1 and ENV2). Seventeen and five genomic regions were mapped by the RHM method in ENV1 and ENV2, respectively. Subsequent genome-wide analysis based on the reference genome B73 revealed associations with forty-six candidate genes within these genomic regions, some of them are considered to be biologically important due to the proteins that they encode. The results obtained by the RHM method have the potential to contribute to knowledge on the genetic architecture of the growth and yield traits of popcorn, which might be used for marker-assisted selection in breeding programs.
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Santantonio N, Jannink JL, Sorrells M. A Low Resolution Epistasis Mapping Approach To Identify Chromosome Arm Interactions in Allohexaploid Wheat. G3 (Bethesda) 2019; 9:675-84. [PMID: 30455184 DOI: 10.1534/g3.118.200646] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Epistasis is an important contributor to genetic variance. In inbred populations, pairwise epistasis is present as additive by additive interactions. Testing for epistasis presents a multiple testing problem as the pairwise search space for modest numbers of markers is large. Single markers do not necessarily track functional units of interacting chromatin as well as haplotype based methods do. To harness the power of multiple markers while minimizing the number of tests conducted, we present a low resolution test for epistatic interactions across whole chromosome arms. Epistasis covariance matrices were constructed from the additive covariances of individual chromosome arms. These covariances were subsequently used to estimate an epistatic variance parameter while correcting for background additive and epistatic effects. We find significant epistasis for 2% of the interactions tested for four agronomic traits in a winter wheat breeding population. Interactions across homeologous chromosome arms were identified, but were less abundant than other chromosome arm pair interactions. The homeologous chromosome arm pair 4BL/4DL showed a strong negative relationship between additive and interaction effects that may be indicative of functional redundancy. Several chromosome arms appeared to act as hubs in an interaction network, suggesting that they may contain important regulatory factors. The differential patterns of epistasis across different traits demonstrate that detection of epistatic interactions is robust when correcting for background additive and epistatic effects in the population. The low resolution epistasis mapping method presented here identifies important epistatic interactions with a limited number of statistical tests at the cost of low precision.
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Resende RT, de Resende MDV, Azevedo CF, Fonseca E Silva F, Melo LC, Pereira HS, Souza TLPO, Valdisser PAMR, Brondani C, Vianello RP. Genome-Wide Association and Regional Heritability Mapping of Plant Architecture, Lodging and Productivity in Phaseolus vulgaris. G3 (Bethesda) 2018; 8:2841-2854. [PMID: 29967054 PMCID: PMC6071601 DOI: 10.1534/g3.118.200493] [Citation(s) in RCA: 14] [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] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/27/2018] [Indexed: 12/13/2022]
Abstract
The availability of high-density molecular markers in common bean has allowed to explore the genetic basis of important complex agronomic traits with increased resolution. Genome-Wide Association Studies (GWAS) and Regional Heritability Mapping (RHM) are two analytical approaches for the detection of genetic variants. We carried out GWAS and RHM for plant architecture, lodging and productivity across two important growing environments in Brazil in a germplasm of 188 common bean varieties using DArTseq genotyping strategies. The coefficient of determination of G × E interaction (c2int ) was equal to 17, 21 and 41%, respectively for the traits architecture, lodging, and productivity. Trait heritabilities were estimated at 0.81 (architecture), 0.79 (lodging) and 0.43 (productivity), and total genomic heritability accounted for large proportions (72% to ≈100%) of trait heritability. At the same probability threshold, three marker-trait associations were detected using GWAS, while RHM detected eight QTL encompassing 145 markers along five chromosomes. The proportion of genomic heritability explained by RHM was considerably higher (35.48 to 58.02) than that explained by GWAS (28.39 to 30.37). In general, RHM accounted for larger fractions of the additive genetic variance being captured by markers effects inside the defined regions. Nevertheless, a considerable proportion of the heritability is still missing (∼42% to ∼64%), probably due to LD between markers and genes and/or rare allele variants not sampled. RHM in autogamous species had the potential to identify larger-effect QTL combining allelic variants that could be effectively incorporated into whole-genome prediction models and tracked through breeding generations using marker-assisted selection.
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Affiliation(s)
| | - Marcos Deon V de Resende
- Department of Forestry
- Department of Statistics, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
- EMBRAPA Florestas, Colombo, PR 83411-000, Brazil
| | - Camila F Azevedo
- Department of Statistics, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | | | | | | | | | | | - Claudio Brondani
- Laboratory of Biotechnology, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, GO 75375-000, Brazil
| | - Rosana Pereira Vianello
- Laboratory of Biotechnology, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, GO 75375-000, Brazil
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