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Baguma JK, Mukasa SB, Nuwamanya E, Alicai T, Omongo CA, Ochwo-Ssemakula M, Ozimati A, Esuma W, Kanaabi M, Wembabazi E, Baguma Y, Kawuki RS. Identification of Genomic Regions for Traits Associated with Flowering in Cassava ( Manihot esculenta Crantz). PLANTS (BASEL, SWITZERLAND) 2024; 13:796. [PMID: 38592820 PMCID: PMC10974989 DOI: 10.3390/plants13060796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 04/11/2024]
Abstract
Flowering in cassava (Manihot esculenta Crantz) is crucial for the generation of botanical seed for breeding. However, genotypes preferred by most farmers are erect and poor at flowering or never flower. To elucidate the genetic basis of flowering, 293 diverse cassava accessions were evaluated for flowering-associated traits at two locations and seasons in Uganda. Genotyping using the Diversity Array Technology Pty Ltd. (DArTseq) platform identified 24,040 single-nucleotide polymorphisms (SNPs) distributed on the 18 cassava chromosomes. Population structure analysis using principal components (PCs) and kinships showed three clusters; the first five PCs accounted for 49.2% of the observed genetic variation. Linkage disequilibrium (LD) estimation averaged 0.32 at a distance of ~2850 kb (kilo base pairs). Polymorphism information content (PIC) and minor allele frequency (MAF) were 0.25 and 0.23, respectively. A genome-wide association study (GWAS) analysis uncovered 53 significant marker-trait associations (MTAs) with flowering-associated traits involving 27 loci. Two loci, SNPs S5_29309724 and S15_11747301, were associated with all the traits. Using five of the 27 SNPs with a Phenotype_Variance_Explained (PVE) ≥ 5%, 44 candidate genes were identified in the peak SNP sites located within 50 kb upstream or downstream, with most associated with branching traits. Eight of the genes, orthologous to Arabidopsis and other plant species, had known functional annotations related to flowering, e.g., eukaryotic translation initiation factor and myb family transcription factor. This study identified genomic regions associated with flowering-associated traits in cassava, and the identified SNPs can be useful in marker-assisted selection to overcome hybridization challenges, like unsynchronized flowering, and candidate gene validation.
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Affiliation(s)
- Julius K. Baguma
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Settumba B. Mukasa
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
| | - Ephraim Nuwamanya
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Titus Alicai
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Christopher Abu Omongo
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
| | - Mildred Ochwo-Ssemakula
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
| | - Alfred Ozimati
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- School of Biological Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Williams Esuma
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
| | - Michael Kanaabi
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Enoch Wembabazi
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Yona Baguma
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
| | - Robert S. Kawuki
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
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Liu H, Yu S. A dimensionality-reduction genomic prediction method without direct inverse of the genomic relationship matrix for large genomic data. PLANT CELL REPORTS 2023; 42:1825-1832. [PMID: 37750948 DOI: 10.1007/s00299-023-03069-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/08/2023] [Indexed: 09/27/2023]
Abstract
KEY MESSAGE A new genomic prediction method (RHPP) was developed via combining randomized Haseman-Elston regression (RHE-reg), PCR based on genomic information of core population, and preconditioned conjugate gradient (PCG) algorithm. Computational efficiency is becoming a hot issue in the practical application of genomic prediction due to the large number of data generated by the high-throughput genotyping technology. In this study, we developed a fast genomic prediction method RHPP via combining randomized Haseman-Elston regression (RHE-reg), PCR based on genomic information of core population, and preconditioned conjugate gradient (PCG) algorithm. The simulation results demonstrated similar prediction accuracy between RHPP and GBLUP, and significantly higher computational efficiency of the former with the increase of individuals. The results of real datasets of both bread wheat and loblolly pine demonstrated that RHPP had a similar or better predictive accuracy in most cases compared with GBLUP. In the future, RHPP may be an attractive choice for analyzing large-scale and high-dimensional data.
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Affiliation(s)
- Hailan Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, Guizhou, China.
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Santos AD, Bandeira e Sousa M, Cunha Alves AA, de Oliveira EJ. Flowering induction in cassava using photoperiod extension premature pruning and plant growth regulators. PLoS One 2023; 18:e0292385. [PMID: 37797072 PMCID: PMC10553807 DOI: 10.1371/journal.pone.0292385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023] Open
Abstract
Cassava (Manihot esculenta Crantz) is a vital crop for food and economic security in many regions of the world. Despite the economic and social importance of cassava, challenges persist in developing superior varieties that meet the needs of farmers in terms of agronomic performance, nutritional quality, and resistance to pests and diseases. One of the main obstacles for genetic improvement is the lack of synchronization in flowering and the abortion of young flowers, making planned crosses and progeny production difficult. Therefore, the aim of this study was to evaluate the effect of photoperiod, premature pruning, and growth regulators on cassava flowering under low-altitude conditions in Brazil. Eight cassava clones with contrasting flowering capacity were assessed in Cruz das Almas, Bahia, using two photoperiods (ambient condition and extended photoperiod with red light for 12 hours), premature pruning at the first and second branching levels (with and without pruning), and the application of growth regulators: 0.5 mM 6-benzyladenine (BA) and 4.0 mM silver thiosulfate (STS) (with and without). Plots were assessed weekly for the number of female (NFF) and male (NMF) flowers, height of the first branching (H1B, in cm), number of days to the first branching (ND1B), and the number of branching events up to 240 days after planting (NOB). The extended photoperiod did not promote an increase in the number of flowers but allowed for precocity in cassava flowering, reducing the onset of flowering by up to 35 days, and significantly increasing the number of branches, which is closely related to flowering. The use of pruning and plant growth regulators (PGR) resulted in an increase in NFF from 2.2 (control) to 4.6 and NMF from 8.1 to 21.1 flowers. Therefore, under hot and humid tropical conditions at low altitudes in the Recôncavo of Bahia, manipulating the photoperiod and using premature pruning and plant growth regulators can accelerate cassava flowering, benefiting genetic improvement programs.
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Juiputta J, Chankitisakul V, Boonkum W. Appropriate Genetic Approaches for Heat Tolerance and Maintaining Good Productivity in Tropical Poultry Production: A Review. Vet Sci 2023; 10:591. [PMID: 37888543 PMCID: PMC10611393 DOI: 10.3390/vetsci10100591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023] Open
Abstract
Heat stress is a major environmental threat to poultry production systems, especially in tropical areas. The effects of heat stress have been discovered in several areas, including reduced growth rate, reduced egg production, low feed efficiency, impaired immunological responses, changes in intestinal microflora, metabolic changes, and deterioration of meat quality. Although several methods have been used to address the heat stress problem, it persists. The answer to this problem can be remedied sustainably if genetic improvement approaches are available. Therefore, the purpose of this review article was to present the application of different approaches to genetic improvement in poultry in the hope that users will find suitable solutions for their poultry population and be able to plan future poultry breeding programs.
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Affiliation(s)
- Jiraporn Juiputta
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
| | - Vibuntita Chankitisakul
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
- Network Center for Animal Breeding and Omics Research, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Wuttigrai Boonkum
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
- Network Center for Animal Breeding and Omics Research, Khon Kaen University, Khon Kaen 40002, Thailand
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Shoormij F, Mirlohi A, Chan-Rodriguez D, Bolibok-Brągoszewska H, Saeidi G. Characterization of 14 Triticum species for the NAM-B1 gene and its associated traits. PLoS One 2023; 18:e0287798. [PMID: 37607184 PMCID: PMC10443865 DOI: 10.1371/journal.pone.0287798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/13/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Wheat grain protein, zinc (Zn), and iron (Fe) content are important wheat qualities crucial for human nutrition and health worldwide. Increasing these three components simultaneously in wheat grains by a single gene came into the picture through NAM-B1 cloning. NAM-B1 gene and its association with the mentioned grain quality traits have been primarily studied in common and durum wheat and their progenitors T. dicoccum and T. dicoccoides. METHOD In the present study, for the first time, 38 wheat accessions comprising ten hexaploids from five species and 28 tetraploids from nine species were evaluated in the field for two consecutive years. Additionally, the 582 first nucleotides of the NAM-B1 gene were examined. RESULT The NAM-B1 gene was present in 21 tetraploids and five hexaploid accessions. Seven tetraploid accessions contained the wild-type allele (five T. dicoccum, one T. dicoccoides, and one T. ispahanicum) and fourteen the mutated allele with a 'T' insertion at position 11 in the open reading frame, causing a frameshift. In hexaploid wheat comprising the gene, only one accession of T. spelta contained the wild-type allele, and the rest resembled the insertion mutated type. In the two-year field experiment, eight accessions with the wild-type NAM-B1 allele had significantly higher protein, Zn and Fe grain content when compared to indel-type accessions. Additionally, these accessions exhibited a lower mean for seed-filling duration than all other accessions containing indel-type alleles. In terms of grain yield, 1,000-kernel weight, kernel diameter, and kernel length, T. dicoccum accessions having wild-type alleles were similar to the indel-type accessions over two years of evaluation. CONCLUSION These findings further support the possibility of simultaneous improvement of wheat grain protein, Zn, and Fe content by a single gene crucial for human nutrition and health worldwide.
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Affiliation(s)
- Fatemeh Shoormij
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Aghafakhr Mirlohi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - David Chan-Rodriguez
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Ghodratollah Saeidi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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Sinha D, Maurya AK, Abdi G, Majeed M, Agarwal R, Mukherjee R, Ganguly S, Aziz R, Bhatia M, Majgaonkar A, Seal S, Das M, Banerjee S, Chowdhury S, Adeyemi SB, Chen JT. Integrated Genomic Selection for Accelerating Breeding Programs of Climate-Smart Cereals. Genes (Basel) 2023; 14:1484. [PMID: 37510388 PMCID: PMC10380062 DOI: 10.3390/genes14071484] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Rapidly rising population and climate changes are two critical issues that require immediate action to achieve sustainable development goals. The rising population is posing increased demand for food, thereby pushing for an acceleration in agricultural production. Furthermore, increased anthropogenic activities have resulted in environmental pollution such as water pollution and soil degradation as well as alterations in the composition and concentration of environmental gases. These changes are affecting not only biodiversity loss but also affecting the physio-biochemical processes of crop plants, resulting in a stress-induced decline in crop yield. To overcome such problems and ensure the supply of food material, consistent efforts are being made to develop strategies and techniques to increase crop yield and to enhance tolerance toward climate-induced stress. Plant breeding evolved after domestication and initially remained dependent on phenotype-based selection for crop improvement. But it has grown through cytological and biochemical methods, and the newer contemporary methods are based on DNA-marker-based strategies that help in the selection of agronomically useful traits. These are now supported by high-end molecular biology tools like PCR, high-throughput genotyping and phenotyping, data from crop morpho-physiology, statistical tools, bioinformatics, and machine learning. After establishing its worth in animal breeding, genomic selection (GS), an improved variant of marker-assisted selection (MAS), has made its way into crop-breeding programs as a powerful selection tool. To develop novel breeding programs as well as innovative marker-based models for genetic evaluation, GS makes use of molecular genetic markers. GS can amend complex traits like yield as well as shorten the breeding period, making it advantageous over pedigree breeding and marker-assisted selection (MAS). It reduces the time and resources that are required for plant breeding while allowing for an increased genetic gain of complex attributes. It has been taken to new heights by integrating innovative and advanced technologies such as speed breeding, machine learning, and environmental/weather data to further harness the GS potential, an approach known as integrated genomic selection (IGS). This review highlights the IGS strategies, procedures, integrated approaches, and associated emerging issues, with a special emphasis on cereal crops. In this domain, efforts have been taken to highlight the potential of this cutting-edge innovation to develop climate-smart crops that can endure abiotic stresses with the motive of keeping production and quality at par with the global food demand.
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Affiliation(s)
- Dwaipayan Sinha
- Department of Botany, Government General Degree College, Mohanpur 721436, India
| | - Arun Kumar Maurya
- Department of Botany, Multanimal Modi College, Modinagar, Ghaziabad 201204, India
| | - Gholamreza Abdi
- Department of Biotechnology, Persian Gulf Research Institute, Persian Gulf University, Bushehr 75169, Iran
| | - Muhammad Majeed
- Department of Botany, University of Gujrat, Punjab 50700, Pakistan
| | - Rachna Agarwal
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Rashmi Mukherjee
- Research Center for Natural and Applied Sciences, Department of Botany (UG & PG), Raja Narendralal Khan Women's College, Gope Palace, Midnapur 721102, India
| | - Sharmistha Ganguly
- Department of Dravyaguna, Institute of Post Graduate Ayurvedic Education and Research, Kolkata 700009, India
| | - Robina Aziz
- Department of Botany, Government, College Women University, Sialkot 51310, Pakistan
| | - Manika Bhatia
- TERI School of Advanced Studies, New Delhi 110070, India
| | - Aqsa Majgaonkar
- Department of Botany, St. Xavier's College (Autonomous), Mumbai 400001, India
| | - Sanchita Seal
- Department of Botany, Polba Mahavidyalaya, Polba 712148, India
| | - Moumita Das
- V. Sivaram Research Foundation, Bangalore 560040, India
| | - Swastika Banerjee
- Department of Botany, Kairali College of +3 Science, Champua, Keonjhar 758041, India
| | - Shahana Chowdhury
- Department of Biotechnology, Faculty of Engineering Sciences, German University Bangladesh, TNT Road, Telipara, Chandona Chowrasta, Gazipur 1702, Bangladesh
| | - Sherif Babatunde Adeyemi
- Ethnobotany/Phytomedicine Laboratory, Department of Plant Biology, Faculty of Life Sciences, University of Ilorin, Ilorin P.M.B 1515, Nigeria
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
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Labroo MR, Endelman JB, Gemenet DC, Werner CR, Gaynor RC, Covarrubias-Pazaran GE. Clonal diploid and autopolyploid breeding strategies to harness heterosis: insights from stochastic simulation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:147. [PMID: 37291402 DOI: 10.1007/s00122-023-04377-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 05/05/2023] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE Reciprocal recurrent selection sometimes increases genetic gain per unit cost in clonal diploids with heterosis due to dominance, but it typically does not benefit autopolyploids. Breeding can change the dominance as well as additive genetic value of populations, thus utilizing heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability. However, the relative performances of RRS and other breeding strategies have not been thoroughly compared. RRS can have relatively increased costs and longer cycle lengths, but these are sometimes outweighed by its ability to harness heterosis due to dominance. Here, we used stochastic simulation to compare genetic gain per unit cost of RRS, terminal crossing, recurrent selection on breeding value, and recurrent selection on cross performance considering different amounts of population heterosis due to dominance, relative cycle lengths, time horizons, estimation methods, selection intensities, and ploidy levels. In diploids with phenotypic selection at high intensity, whether RRS was the optimal breeding strategy depended on the initial population heterosis. However, in diploids with rapid-cycling genomic selection at high intensity, RRS was the optimal breeding strategy after 50 years over almost all amounts of initial population heterosis under the study assumptions. Diploid RRS required more population heterosis to outperform other strategies as its relative cycle length increased and as selection intensity and time horizon decreased. The optimal strategy depended on selection intensity, a proxy for inbreeding rate. Use of diploid fully inbred parents vs. outbred parents with RRS typically did not affect genetic gain. In autopolyploids, RRS typically did not outperform one-pool strategies regardless of the initial population heterosis.
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Affiliation(s)
- Marlee R Labroo
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jeffrey B Endelman
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dorcus C Gemenet
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Christian R Werner
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Giovanny E Covarrubias-Pazaran
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico.
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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Lebot V, Lawac F, Muñoz-Cuervo I, Mercier PE, Legendre L. Metabolite fingerprinting of cassava (Manihot esculenta Crantz) landraces assessed for post-harvest physiological deterioration (PPD). Food Chem 2023; 421:136217. [PMID: 37121018 DOI: 10.1016/j.foodchem.2023.136217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/02/2023]
Abstract
Cassava landraces are impacted by post-harvest physiological deterioration (PPD). 34 primary/secondary metabolites (carotenes, flavonols, indols, phenolic, hydroxycinnamic, and organic acids) were analysed using HPLC/GC-MS in 72 landraces harvested 8 months after planting (MAP) to clarify whether these compounds may play a role in PPD tolerance. Cluster analysis differentiated a first group with high organic acids contents, citric acid being dominant, a second group with landraces high in tryptophan, a third group including landraces with high phenolic and hydroxycinnamic acids content, and a fourth group characterised by 8 carotenoids. PPD tolerant and susceptible landraces were present in each group. To determine if PPD is related to age of harvest, 174 landraces were harvested at 6, 8, 10 and 12 MAP. Scopoletin, sucrose and glucose were analysed. PPD was positively correlated with DMC and negatively correlated with scopoletin at all ages of harvest. Scopoletin is a useful biomarker to characterize landraces.
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Affiliation(s)
- Vincent Lebot
- CIRAD-VARTC, P.O. Box 946, Port-Vila, Vanuatu; UMR AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France.
| | | | - Ismaël Muñoz-Cuervo
- Université Claude Bernard Lyon 1, Laboratoire d'Écologie Microbienne, Équipe 3 - Rhizosphère, CESN (Centre d'Étude des Substances Naturelles), France; UMR UCBL CNRS 5557 - INRA 1418. 16 rue Raphaël Dubois. F-69100 Villeurbanne Cedex, France
| | - Pierre-Edouard Mercier
- Université Claude Bernard Lyon 1, Laboratoire d'Écologie Microbienne, Équipe 3 - Rhizosphère, CESN (Centre d'Étude des Substances Naturelles), France; UMR UCBL CNRS 5557 - INRA 1418. 16 rue Raphaël Dubois. F-69100 Villeurbanne Cedex, France.
| | - Laurent Legendre
- Université Claude Bernard Lyon 1, Laboratoire d'Écologie Microbienne, Équipe 3 - Rhizosphère, CESN (Centre d'Étude des Substances Naturelles), France; UMR UCBL CNRS 5557 - INRA 1418. 16 rue Raphaël Dubois. F-69100 Villeurbanne Cedex, France.
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Zhang M, Chen Y, Xing H, Ke W, Shi Y, Sui Z, Xu R, Gao L, Guo G, Li J, Xing J, Zhang Y. Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:772-790. [PMID: 36354146 DOI: 10.1111/jipb.13408] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Lateral roots play essential roles in drought tolerance in maize (Zea mays L.). However, the genetic basis for the variation in the number of lateral roots in maize remains elusive. Here, we identified a major quantitative trait locus (QTL), qLRT5-1, controlling lateral root number using a recombinant inbred population from a cross between the maize lines Zong3 (with many lateral roots) and 87-1 (with few lateral roots). Fine-mapping and functional analysis determined that the candidate gene for qLRT5-1, ZmLRT, expresses the primary transcript for the microRNA miR166a. ZmLRT was highly expressed in root tips and lateral root primordia, and knockout and overexpression of ZmLRT increased and decreased lateral root number, respectively. Compared with 87-1, the ZmLRT gene model of Zong3 lacked the second and third exons and contained a 14 bp deletion at the junction between the first exon and intron, which altered the splicing site. In addition, ZmLRT expression was significantly lower in Zong3 than in 87-1, which might be attributed to the insertions of a transposon and over large DNA fragments in the Zong3 ZmLRT promoter region. These mutations decreased the abundance of mature miR166a in Zong3, resulting in increased lateral roots at the seedling stage. Furthermore, miR166a post-transcriptionally repressed five development-related class-III homeodomain-leucine zipper genes. Moreover, knockout of ZmLRT enhanced drought tolerance of maize seedlings. Our study furthers our understanding of the genetic basis of lateral root number variation in maize and highlights ZmLRT as a target for improving drought tolerance in maize.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yanhong Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Agronomy College of Shandong Agricultural University, Taian, 271018, China
| | - Hongyan Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wensheng Ke
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yunlu Shi
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhipeng Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Yantai Science and Technology Innovation Promotion Center, Yantai, 264003, China
| | - Ruibin Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Lulu Gao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Ganggang Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yirong Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
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10
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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. THE PLANT CELL 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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11
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Esuma W, Eyoo O, Gwandu F, Mukasa S, Alicai T, Ozimati A, Nuwamanya E, Rabbi I, Kawuki R. Validation of KASP markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:1017275. [PMID: 36507387 PMCID: PMC9727383 DOI: 10.3389/fpls.2022.1017275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION The intrinsic high heterozygosity of cassava makes conventional breeding ineffective for rapid genetic improvement. However, recent advances in next generation sequencing technologies have enabled the use of high-density markers for genome-wide association studies, aimed at identifying single nucleotide polymorphisms (SNPs) linked to major traits such as cassava mosaic disease (CMD) resistance, dry matter content (DMC) and total carotenoids content (TCC). A number of these trait-linked SNPs have been converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers for downstream application of marker assisted selection. METHODS We assayed 13 KASP markers to evaluate their effectiveness in selecting for CMD, DMC and TCC in 1,677 diverse cassava genotypes representing two independent breeding populations in Uganda. RESULTS Five KASP markers had significant co-segregation with phenotypes; CMD resistance (2), DMC (1) and TCC (2), with each marker accounting for at least 30% of the phenotypic variation. Markers located within the chromosomal regions for which strong marker-trait association loci have been characterised (chromosome 12 markers for CMD, chromosome 1 markers for DMC and TCC) had consistently superior ability to discriminate the respective phenotypes. DISCUSSION The results indicate varying discriminatory abilities of the KASP markers assayed and the need for their context-based use for MAS, with PSY2_572 particularly effective in selecting for high TCC. Availing the effective KASP markers on cost-effective genotyping platforms could facilitate practical implementation of marker-assisted cassava breeding for accelerated genetic gains for CMD, DMC and provitamin A carotenoids.
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Affiliation(s)
- Williams Esuma
- National Crops Resources Research Institute, Kampala, Uganda
| | - Oscar Eyoo
- National Crops Resources Research Institute, Kampala, Uganda
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | - Francisca Gwandu
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | - Settumba Mukasa
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | - Titus Alicai
- National Crops Resources Research Institute, Kampala, Uganda
| | - Alfred Ozimati
- National Crops Resources Research Institute, Kampala, Uganda
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | | | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), Oyo, Nigeria
| | - Robert Kawuki
- National Crops Resources Research Institute, Kampala, Uganda
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12
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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. FRONTIERS IN PLANT SCIENCE 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] [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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13
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Ni P, Anche MT, Ruan Y, Dang D, Morales N, Li L, Liu M, Wang S, Robbins KR. Genomic Prediction Strategies for Dry-Down-Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:930429. [PMID: 35845649 PMCID: PMC9280646 DOI: 10.3389/fpls.2022.930429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
For efficient mechanical harvesting, low grain moisture content at harvest time is essential. Dry-down rate (DR), which refers to the reduction in grain moisture content after the plants enter physiological maturity, is one of the main factors affecting the amount of moisture in the kernels. Dry-down rate is estimated using kernel moisture content at physiological maturity and at harvest time; however, measuring kernel water content at physiological maturity, which is sometimes referred as kernel water content at black layer formation (BWC), is time-consuming and resource-demanding. Therefore, inferring BWC from other correlated and easier to measure traits could improve the efficiency of breeding efforts for dry-down-related traits. In this study, multi-trait genomic prediction models were used to estimate genetic correlations between BWC and water content at harvest time (HWC) and flowering time (FT). The results show there is moderate-to-high genetic correlation between the traits (0.24-0.66), which supports the use of multi-trait genomic prediction models. To investigate genomic prediction strategies, several cross-validation scenarios representing possible implementations of genomic prediction were evaluated. The results indicate that, in most scenarios, the use of multi-trait genomic prediction models substantially increases prediction accuracy. Furthermore, the inclusion of historical records for correlated traits can improve prediction accuracy, even when the target trait is not measured on all the plots in the training set.
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Affiliation(s)
- Pengzun Ni
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Liaoning Province Research Center of Plant Genetic Engineering Technology, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Mahlet Teka Anche
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
| | - Yanye Ruan
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Liaoning Province Research Center of Plant Genetic Engineering Technology, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Dongdong Dang
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Liaoning Province Research Center of Plant Genetic Engineering Technology, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Nicolas Morales
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
| | - Lingyue Li
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Liaoning Province Research Center of Plant Genetic Engineering Technology, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Meiling Liu
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Liaoning Province Research Center of Plant Genetic Engineering Technology, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Shu Wang
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Kelly R. Robbins
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
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14
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Schoffel A, Lopes SJ, Koefender J, Lúcio AD, Camera JN, Golle DP. Adaptation of rapid multiplication method: cassava stem and root yield at different spacings and transplanting seasons. AN ACAD BRAS CIENC 2022; 94:e20191273. [PMID: 35703686 DOI: 10.1590/0001-3765202220191273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/31/2021] [Indexed: 11/22/2022] Open
Abstract
This study aimed to assess cassava root and stem yield at different spacings and four transplanting seasons of seedlings produced by an adaptation of the rapid multiplication method. The experimental design was a randomized block design with three replications in a factorial (4 × 5) arranged in strips. Treatments consisted of the combinations of growing seasons (November 9 and 24 and December 3 and 26) and spacings (0.6 × 0.6, 0.8 × 0.8, 0.8 × 0.6, 1.0 × 0.6, and 1.0 × 0.8 m). The percentage of survival, main stem branching height, number of branches, base, middle, and upper diameter, mean diameter, stem length, number of buds per stem and hectare, root length and diameter, root fresh matter per plant and hectare, and number of roots per plant were measured at harvest. Seedling transplanting performed up to November 24 favored the expression of stem and root yield. The spacing of 1.0 × 0.6 m was the most suitable for stem yield traits.
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Affiliation(s)
- André Schoffel
- Universidade Federal de Santa Maria, Avenida Roraima, 1000, 97105-900 Santa Maria, RS, Brazil
| | - Sidinei J Lopes
- Universidade Federal de Santa Maria, Avenida Roraima, 1000, 97105-900 Santa Maria, RS, Brazil
| | - Jana Koefender
- Universidade de Cruz Alta, Rodovia Jacob Della Méa, Km 5.6, 98005-972 Cruz Alta, RS,Brazil
| | - Alessandro D Lúcio
- Universidade Federal de Santa Maria, Avenida Roraima, 1000, 97105-900 Santa Maria, RS, Brazil
| | - Juliane N Camera
- Universidade de Cruz Alta, Rodovia Jacob Della Méa, Km 5.6, 98005-972 Cruz Alta, RS,Brazil
| | - Diego P Golle
- Universidade de Cruz Alta, Rodovia Jacob Della Méa, Km 5.6, 98005-972 Cruz Alta, RS,Brazil
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15
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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 MOLECULAR BIOLOGY 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] [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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16
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Tripathi L, Dhugga KS, Ntui VO, Runo S, Syombua ED, Muiruri S, Wen Z, Tripathi JN. Genome Editing for Sustainable Agriculture in Africa. Front Genome Ed 2022; 4:876697. [PMID: 35647578 PMCID: PMC9133388 DOI: 10.3389/fgeed.2022.876697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/21/2022] [Indexed: 12/25/2022] Open
Abstract
Sustainable intensification of agriculture in Africa is essential for accomplishing food and nutritional security and addressing the rising concerns of climate change. There is an urgent need to close the yield gap in staple crops and enhance food production to feed the growing population. In order to meet the increasing demand for food, more efficient approaches to produce food are needed. All the tools available in the toolbox, including modern biotechnology and traditional, need to be applied for crop improvement. The full potential of new breeding tools such as genome editing needs to be exploited in addition to conventional technologies. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing has rapidly become the most prevalent genetic engineering approach for developing improved crop varieties because of its simplicity, efficiency, specificity, and easy to use. Genome editing improves crop variety by modifying its endogenous genome free of any foreign gene. Hence, genome-edited crops with no foreign gene integration are not regulated as genetically modified organisms (GMOs) in several countries. Researchers are using CRISPR/Cas-based genome editing for improving African staple crops for biotic and abiotic stress resistance and improved nutritional quality. Many products, such as disease-resistant banana, maize resistant to lethal necrosis, and sorghum resistant to the parasitic plant Striga and enhanced quality, are under development for African farmers. There is a need for creating an enabling environment in Africa with science-based regulatory guidelines for the release and adoption of the products developed using CRISPR/Cas9-mediated genome editing. Some progress has been made in this regard. Nigeria and Kenya have recently published the national biosafety guidelines for the regulation of gene editing. This article summarizes recent advances in developments of tools, potential applications of genome editing for improving staple crops, and regulatory policies in Africa.
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Affiliation(s)
- Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- *Correspondence: Leena Tripathi,
| | | | - Valentine O. Ntui
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | | | - Easter D. Syombua
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Samwel Muiruri
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- Kenyatta University, Nairobi, Kenya
| | - Zhengyu Wen
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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17
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Utsumi Y, Utsumi C, Tanaka M, Takahashi S, Okamoto Y, Ono M, Nakamura Y, Seki M. Suppressed expression of starch branching enzyme 1 and 2 increases resistant starch and amylose content and modifies amylopectin structure in cassava. PLANT MOLECULAR BIOLOGY 2022; 108:413-427. [PMID: 34767147 DOI: 10.1007/s11103-021-01209-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Suppression of starch branching enzymes 1 and 2 in cassava leads to increased resistant starch content through the production of high-amylose and modification of the amylopectin structure. Cassava (Manihot esculenta Crantz) is a starchy root crop used for human consumption as a staple food and industrial applications. Starch is synthesized by various isoforms of several enzymes. However, the function of starch branching enzymes (SBEs) in starch biosynthesis and mechanisms of starch regulation in cassava have not been understood well. In this study, we aimed to suppress the expression of SBEs in cassava to generate starches with a range of distinct properties, in addition to verifying the functional characteristics of the SBEs. One SBE1, two SBE2, and one SBE3 genes were classified by phylogenetic analysis and amino acid alignment. Quantitative real-time RT-PCR revealed tissue-specific expression of SBE genes in the tuberous roots and leaves of cassava. We introduced RNAi constructs containing fragments of SBE1, SBE2, or both genes into cassava by Agrobacterium-mediated transformation, and assessed enzymatic activity of SBE using tuberous roots and leaves from these transgenic plants. Simultaneous suppression of SBE1 and SBE2 rendered an extreme starch phenotype compared to suppression of SBE2 alone. Degree of polymerization of 6-13 chains in amylopectin was markedly reduced by suppression of both SBE1 and SBE2 in comparison to the SBE2 suppression; however, no change in chain-length profiles was observed in the SBE1 suppression alone. The role of SBE1 and SBE2 may have functional overlap in the storage tissue of cassava. Simultaneous suppression of SBE1 and SBE2 resulted in highly resistant starch with increased apparent amylose content compared to suppression of SBE2 alone. This study provides valuable information for understanding starch biosynthesis and suggests targets for altering starch quality.
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Affiliation(s)
- Yoshinori Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Chikako Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Satoshi Takahashi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshie Okamoto
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Masami Ono
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-nishi, Shimoshinjo-Nakano, Akita, 010-0195, Japan
- Akita Natural Science Laboratory, 25-44 Oiwake-Nishi, Tennoh, Katagami, Akita, 010-0101, Japan
| | - Yasunori Nakamura
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-nishi, Shimoshinjo-Nakano, Akita, 010-0195, Japan
- Akita Natural Science Laboratory, 25-44 Oiwake-Nishi, Tennoh, Katagami, Akita, 010-0101, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7- 22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan.
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18
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Pierre N, Wamalwa LN, Muiru WM, Simon B, Kanju E, Ferguson ME, Ndavi MM, Tumwegamire S. Genetic diversity of local and introduced cassava germplasm in Burundi using DArTseq molecular analyses. PLoS One 2022; 17:e0256002. [PMID: 35073332 PMCID: PMC8786168 DOI: 10.1371/journal.pone.0256002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/16/2021] [Indexed: 11/19/2022] Open
Abstract
In Burundi most small-scale farmers still grow traditional cassava landraces that are adapted to local conditions and have been selected for consumer preferred attributes. They tend to be susceptible, in varying degrees, to devastating cassava viral diseases such as Cassava Brown Streak Disease (CBSD) and Cassava Mosaic Disease (CMD) with annual production losses of US$1 billion. For long term resistance to the disease, several breeding strategies have been proposed. A sound basis for a breeding program is to understand the genetic diversity of both landraces and elite introduced breeding cultivars. This will also assist in efforts to conserve landraces ahead of the broad distribution of improved varieties which have the possibility of replacing landraces. Our study aimed at determining the genetic diversity and relationships within and between local landraces and introduced elite germplasm using morphological and single nucleotide polymorphism (SNP) markers. A total of 118 cultivars were characterized for morphological trait variation based on leaf, stem and root traits, and genetic variation using SNP markers. Results of morphological characterization based on Ward’s Method revealed three main clusters and five accessions sharing similar characteristics. Molecular characterization identified over 18,000 SNPs and six main clusters and three pairs of duplicates which should be pooled together as one cultivar to avoid redundancy. Results of population genetic analysis showed low genetic distance between populations and between local landraces and elite germplasm. Accessions that shared similar morphological traits were divergent at the molecular level indicating that clustering using morphological traits was inconsistent. Despite the variabilities found within the collection, it was observed that cassava germplasm in Burundi have a narrow genetic base.
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Affiliation(s)
- Niyonzima Pierre
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
- Institut des Sciences Agronomiques du Burundi (ISABU), Bujumbura, Burundi
- * E-mail: ,
| | - Lydia Nanjala Wamalwa
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - William Maina Muiru
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Bigirimana Simon
- Institut des Sciences Agronomiques du Burundi (ISABU), Bujumbura, Burundi
| | - Edward Kanju
- International Institute of Tropical Agriculture (IITA), Kampala, Uganda
| | | | - Malu Muia Ndavi
- International Fund for Agriculture Development (IFAD), Rome, Italy
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19
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Semagn K, Iqbal M, Crossa J, Jarquin D, Howard R, Chen H, Bemister DH, Beres BL, Randhawa H, N'Diaye A, Pozniak C, Spaner D. Genome-based prediction of agronomic traits in spring wheat under conventional and organic management systems. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:537-552. [PMID: 34724078 DOI: 10.1007/s00122-021-03982-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Using phenotype data of three spring wheat populations evaluated at 6-15 environments under two management systems, we found moderate to very high prediction accuracies across seven traits. The phenotype data collected under an organic management system effectively predicted the performance of lines in the conventional management and vice versa. There is growing interest in developing wheat cultivars specifically for organic agriculture, but we are not aware of the effect of organic management on the predictive ability of genomic selection (GS). Here, we evaluated within populations prediction accuracies of four GS models, four combinations of training and testing sets, three reaction norm models, and three random cross-validations (CV) schemes in three populations phenotyped under organic and conventional management systems. Our study was based on a total of 578 recombinant inbred lines and varieties from three spring wheat populations, which were evaluated for seven traits at 3-9 conventionally and 3-6 organically managed field environments and genotyped either with the wheat 90 K SNP array or DArTseq. We predicted the management systems (CV0M) or environments (CV0), a subset of lines that have been evaluated in either management (CV2M) or some environments (CV2), and the performance of newly developed lines in either management (CV1M) or environments (CV1). The average prediction accuracies of the model that incorporated genotype × environment interactions with CV0 and CV2 schemes varied from 0.69 to 0.97. In the CV1 and CV1M schemes, prediction accuracies ranged from - 0.12 to 0.77 depending on the reaction norm models, the traits, and populations. In most cases, grain protein showed the highest prediction accuracies. The phenotype data collected under the organic management effectively predicted the performance of lines under conventional management and vice versa. This is the first comprehensive GS study that investigated the effect of the organic management system in wheat.
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Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Muhammad Iqbal
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - José Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Diego Jarquin
- University of Nebraska - Lincoln, Lincoln, NE, 68583, USA
| | - Reka Howard
- University of Nebraska - Lincoln, Lincoln, NE, 68583, USA
| | - Hua Chen
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, Sichuan, China
| | - Darcy H Bemister
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Brian L Beres
- Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Harpinder Randhawa
- Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food, and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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20
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The combined effect of thermal-acid hydrolysis, periodate oxidation, and iodine species removal on the properties of native tapioca (Manihot esculenta Crantz) starch. Int J Biol Macromol 2022; 196:107-119. [PMID: 34910925 DOI: 10.1016/j.ijbiomac.2021.11.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/08/2021] [Accepted: 11/30/2021] [Indexed: 11/21/2022]
Abstract
Through a four-step top-down approach, native tapioca starch (NTS) was thermally acid-hydrolyzed, periodate-oxidized with subsequent removal of iodine species (i.e., IO4(-), IO3(-), I(-), and I2), and dialdehyde tapioca starch (DTS) alcohol-precipitation. The percent yield was ∼91%. Analyses confirmed the presence of aldehydic functionalities (∼71%), effectual iodine species removal (∼98%), and enhanced water-solubility (∼96.57%). Besides, the combined treatment significantly reduced the Mw (∼57.81 kDa) and ameliorated homogeneity as well as thermal stability (Tmax ∼ 667.15 °C). Structural-spectral characterization also confirmed the presence of aldehydic functionality, polymorphic transition (C- to A-type), and a higher degree of crystallinity (∼91.77%), the latter further corroborated by thermal analysis. The morphological study revealed that the combined treatment reduced size (∼393.55-nm-diameter and ∼5.22-μm-length) and changed shape into rod-like crystals. DTS showed considerably and significantly low cytotoxicity to HaCaT cells in vitro at the concentrations assayed over the test period (24 h). DTS's conformation was most stable at -289 kcal/mol and -151.7 au heat formation and minimum potential energies, respectively. Overall, these results demonstrated that the combined treatment had no deleterious effects on NTS's properties, thus yielded DTS with ideal properties for multifarious uses.
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21
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Hale B, Ferrie AMR, Chellamma S, Samuel JP, Phillips GC. Androgenesis-Based Doubled Haploidy: Past, Present, and Future Perspectives. FRONTIERS IN PLANT SCIENCE 2022; 12:751230. [PMID: 35069615 PMCID: PMC8777211 DOI: 10.3389/fpls.2021.751230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/22/2021] [Indexed: 05/03/2023]
Abstract
Androgenesis, which entails cell fate redirection within the microgametophyte, is employed widely for genetic gain in plant breeding programs. Moreover, androgenesis-responsive species provide tractable systems for studying cell cycle regulation, meiotic recombination, and apozygotic embryogenesis within plant cells. Past research on androgenesis has focused on protocol development with emphasis on temperature pretreatments of donor plants or floral buds, and tissue culture optimization because androgenesis has different nutritional requirements than somatic embryogenesis. Protocol development for new species and genotypes within responsive species continues to the present day, but slowly. There is more focus presently on understanding how protocols work in order to extend them to additional genotypes and species. Transcriptomic and epigenetic analyses of induced microspores have revealed some of the cellular and molecular responses required for or associated with androgenesis. For example, microRNAs appear to regulate early microspore responses to external stimuli; trichostatin-A, a histone deacetylase inhibitor, acts as an epigenetic additive; ά-phytosulfokine, a five amino acid sulfated peptide, promotes androgenesis in some species. Additionally, present work on gene transfer and genome editing in microspores suggest that future endeavors will likely incorporate greater precision with the genetic composition of microspores used in doubled haploid breeding, thus likely to realize a greater impact on crop improvement. In this review, we evaluate basic breeding applications of androgenesis, explore the utility of genomics and gene editing technologies for protocol development, and provide considerations to overcome genotype specificity and morphogenic recalcitrance in non-model plant systems.
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Affiliation(s)
- Brett Hale
- Molecular Biosciences Graduate Program, Arkansas State University, Jonesboro, AR, United States
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, United States
| | | | | | | | - Gregory C. Phillips
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, United States
- College of Agriculture, Arkansas State University, Jonesboro, AR, United States
- Agricultural Experiment Station, University of Arkansas System Division of Agriculture, Jonesboro, AR, United States
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22
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Sánchez FJ, Arciniegas JP, Brand A, Vacca O, Mosquera AJ, Medina A, Chavarriaga P. Metabolic engineering of cassava to improve carotenoids. Methods Enzymol 2022; 671:31-62. [DOI: 10.1016/bs.mie.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Phumichai C, Aiemnaka P, Nathaisong P, Hunsawattanakul S, Fungfoo P, Rojanaridpiched C, Vichukit V, Kongsil P, Kittipadakul P, Wannarat W, Chunwongse J, Tongyoo P, Kijkhunasatian C, Chotineeranat S, Piyachomkwan K, Wolfe MD, Jannink JL, Sorrells ME. Genome-wide association mapping and genomic prediction of yield-related traits and starch pasting properties in cassava. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:145-171. [PMID: 34661695 DOI: 10.1007/s00122-021-03956-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
GWAS identified eight yield-related, peak starch type of waxy and wild-type starch and 21 starch pasting property-related traits (QTLs). Prediction ability of eight GS models resulted in low to high predictability, depending on trait, heritability, and genetic architecture. Cassava is both a food and an industrial crop in Africa, South America, and Asia, but knowledge of the genes that control yield and starch pasting properties remains limited. We carried out a genome-wide association study to clarify the molecular mechanisms underlying these traits and to explore marker-based breeding approaches. We estimated the predictive ability of genomic selection (GS) using parametric, semi-parametric, and nonparametric GS models with a panel of 276 cassava genotypes from Thai Tapioca Development Institute, International Center for Tropical Agriculture, International Institute of Tropical Agriculture, and other breeding programs. The cassava panel was genotyped via genotyping-by-sequencing, and 89,934 single-nucleotide polymorphism (SNP) markers were identified. A total of 31 SNPs associated with yield, starch type, and starch properties traits were detected by the fixed and random model circulating probability unification (FarmCPU), Bayesian-information and linkage-disequilibrium iteratively nested keyway and compressed mixed linear model, respectively. GS models were developed, and forward predictabilities using all the prediction methods resulted in values of - 0.001-0.71 for the four yield-related traits and 0.33-0.82 for the seven starch pasting property traits. This study provides additional insight into the genetic architecture of these important traits for the development of markers that could be used in cassava breeding programs.
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Affiliation(s)
- Chalermpol Phumichai
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand.
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
- Center of Excellence On Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok, 10900, Thailand.
| | - Pornsak Aiemnaka
- Thai Tapioca Development Institute, Lumpini Tower, 1168/26 Rama IV Road, Bangkok, 10120, Thailand
| | - Piyaporn Nathaisong
- Thai Tapioca Development Institute, Lumpini Tower, 1168/26 Rama IV Road, Bangkok, 10120, Thailand
| | - Sirikan Hunsawattanakul
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Center of Excellence On Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok, 10900, Thailand
| | - Phasakorn Fungfoo
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Vichan Vichukit
- Thai Tapioca Development Institute, Lumpini Tower, 1168/26 Rama IV Road, Bangkok, 10120, Thailand
| | - Pasajee Kongsil
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Piya Kittipadakul
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Wannasiri Wannarat
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Julapark Chunwongse
- Department of Horticulture, Faculty of Agriculture Kamphaeng Saen, Kasetsart University, Nakhon Pathom, 73140, Thailand
| | - Pumipat Tongyoo
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Chookiat Kijkhunasatian
- Cassava and Starch Technology Research Team, National Center for Genetic Engineering and Biotechnology, Pathumthani, 12120, Thailand
| | - Sunee Chotineeranat
- Cassava and Starch Technology Research Team, National Center for Genetic Engineering and Biotechnology, Pathumthani, 12120, Thailand
| | - Kuakoon Piyachomkwan
- Cassava and Starch Technology Research Team, National Center for Genetic Engineering and Biotechnology, Pathumthani, 12120, Thailand
| | - Marnin D Wolfe
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, 14850, USA
| | - Jean-Luc Jannink
- United States Department of Agriculture - Agriculture Research Service, Ithaca, NY, 14850, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, 14850, USA
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24
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Uchendu K, Njoku DN, Paterne A, Rabbi IY, Dzidzienyo D, Tongoona P, Offei S, Egesi C. Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava. FRONTIERS IN PLANT SCIENCE 2021; 12:770434. [PMID: 34975953 PMCID: PMC8719520 DOI: 10.3389/fpls.2021.770434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.
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Affiliation(s)
- Kelechi Uchendu
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | | | - Agre Paterne
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Daniel Dzidzienyo
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Samuel Offei
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
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25
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Bhat JA, Yu D, Bohra A, Ganie SA, Varshney RK. Features and applications of haplotypes in crop breeding. Commun Biol 2021; 4:1266. [PMID: 34737387 PMCID: PMC8568931 DOI: 10.1038/s42003-021-02782-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/09/2021] [Indexed: 12/17/2022] Open
Abstract
Climate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop breeding efficiency and delivering better varieties. Fast-growing capacity and affordability of DNA sequencing has motivated large-scale germplasm sequencing projects, thus opening exciting avenues for mining haplotypes for breeding applications. This review article highlights ways to mine haplotypes and apply them for complex trait dissection and in GAB approaches including haplotype-GWAS, haplotype-based breeding, haplotype-assisted genomic selection. Improvement strategies that efficiently deploy superior haplotypes to hasten breeding progress will be key to safeguarding global food security.
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Affiliation(s)
- Javaid Akhter Bhat
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Abhishek Bohra
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research (ICAR- IIPR), Kanpur, India
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, WB, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
- State Agricultural Biotechnology Centre, Centre for Crop & Food Research Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.
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26
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Ceballos H, Hershey C, Iglesias C, Zhang X. Fifty years of a public cassava breeding program: evolution of breeding objectives, methods, and decision-making processes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2335-2353. [PMID: 34086085 PMCID: PMC8277603 DOI: 10.1007/s00122-021-03852-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/03/2021] [Indexed: 06/01/2023]
Abstract
This paper reviews and analyzes key features from cassava breeding at the International Center for Tropical Agriculture (CIAT) over 50 years and draws lessons for public breeding efforts broadly. The breeding team, jointly with national program partners and the private processing sector, defined breeding objectives and guiding business plans. These have evolved through the decades and currently focus on four global product profiles. The recurrent selection method also evolved and included innovations such as estimation of phenotypic breeding values, increasing the number of locations in the first stage of agronomic evaluations, gradual reduction of the duration of breeding cycles (including rapid cycling for high-heritability traits), the development of protocols for the induction of flowering, and the introduction of genome-wide predictions. The impact of cassava breeding depends significantly on the type of target markets. When roots are used for large processing facilities for starch, animal feeding or ethanol production (such as in SE Asia), the adoption of improved varieties is nearly universal and productivity at the regional scale increases significantly. When markets and relevant infrastructure are weak or considerable proportion of the production goes for local artisanal processing and on-farm consumption, the impact has been lower. The potential of novel breeding tools needs to be properly assessed for the most effective allocation of resources. Finally, a brief summary of challenges and opportunities for the future of cassava breeding is presented. The paper describes multiple ways that public and private sector breeding programs can learn from each other to optimize success.
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Affiliation(s)
- Hernán Ceballos
- International Center for Tropical Agriculture (CIAT), Cali, USA.
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Alliance, Rome, Italy.
| | | | | | - Xiaofei Zhang
- International Center for Tropical Agriculture (CIAT), Cali, USA
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Alliance, Rome, Italy
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27
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Jubin C, Griebel S, Beissinger T. Improving genomic tools for outcrossing crops. MOLECULAR PLANT 2021; 14:538-540. [PMID: 33753305 DOI: 10.1016/j.molp.2021.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Cathy Jubin
- Division of Plant Breeding Methodology & Center for Integrated Breeding Research, Department of Crop Science, University of Göttingen, 37075 Göttingen, Germany
| | - Stefanie Griebel
- Division of Plant Breeding Methodology & Center for Integrated Breeding Research, Department of Crop Science, University of Göttingen, 37075 Göttingen, Germany
| | - Timothy Beissinger
- Division of Plant Breeding Methodology & Center for Integrated Breeding Research, Department of Crop Science, University of Göttingen, 37075 Göttingen, Germany.
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28
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Marker-assisted selection complements phenotypic screening at seedling stage to identify cassava mosaic disease-resistant genotypes in African cassava populations. Sci Rep 2021; 11:2850. [PMID: 33531574 PMCID: PMC7854622 DOI: 10.1038/s41598-021-82360-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/14/2021] [Indexed: 11/16/2022] Open
Abstract
Cassava mosaic disease (CMD) is a serious threat to cassava production in sub-Saharan Africa. The use of genomic-assisted selection at the seedling trial stage would help to reduce the time for release, breeding cost, and resources used, hence increase selection efficiency in cassava breeding programs. Five cassava populations were screened for resistance to CMD during the seedling evaluation trial at 1, 3, and 5 months after planting using a scale of 1–5. The genotypes in the five populations were also screened using six molecular markers linked to the CMD2 gene. The correlation between the phenotypic and marker data was estimated. Based on Cassava Mosaic Disease Severity Score (CMDSS), between 53 and 82% of the progenies were resistant across the populations with an average of 70.5%. About 70% of the progenies were identified to be resistant to the disease across the populations with a range of 62–80% using the marker data. With both marker data and CMDSS combined, 40–60% of the progenies in each population, with an average of 52%, were identified to be resistant to CMD. There was a fairly significant correlation between the marker data and CMDSS in each cassava population with correlation coefficients ranging from 0.2024 to 0.3460 suggesting that novel genes not associated to the markers used might be involved in the resistance to CMD. The resistant genotypes identified in this study with potential for other desirable traits were selected for evaluation at the advanced trial stage thereby shortening the period required for the breeding program.
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Kushanov FN, Turaev OS, Ernazarova DK, Gapparov BM, Oripova BB, Kudratova MK, Rafieva FU, Khalikov KK, Erjigitov DS, Khidirov MT, Kholova MD, Khusenov NN, Amanboyeva RS, Saha S, Yu JZ, Abdurakhmonov IY. Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton ( Gossypium spp.). FRONTIERS IN PLANT SCIENCE 2021; 12:779386. [PMID: 34975965 PMCID: PMC8716771 DOI: 10.3389/fpls.2021.779386] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023]
Abstract
Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
- *Correspondence: Fakhriddin N. Kushanov, ;
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Kuvandik K. Khalikov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Doston Sh. Erjigitov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Naim N. Khusenov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Roza S. Amanboyeva
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Sukumar Saha
- Crop Science Research Laboratory, USDA-ARS, Washington, DC, United States
| | - John Z. Yu
- Southern Plains Agricultural Research Center, USDA-ARS, Washington, DC, United States
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
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Chatukuta P, Rey MEC. A cassava protoplast system for screening genes associated with the response to South African cassava mosaic virus. Virol J 2020; 17:184. [PMID: 33228712 PMCID: PMC7685591 DOI: 10.1186/s12985-020-01453-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023] Open
Abstract
Background The study of transient gene expression in cassava plants during virus infection using existing protocols is laborious and may take approximately fifteen weeks due to cassava’s recalcitrance to transformation. The combination of a protoplast system with CRISPR-mediated gene editing promises to shorten the turnaround time from plant tissue culture to high-throughput gene expression screening for candidate genes. Here, we detail a protocol for screening genes associated with the response to South African cassava mosaic virus (SACMV) in cassava protoplasts, with reference to the ubiquitin E3 ligase gene, MeE3L.
Methods Cassava protoplasts of model, and SACMV-susceptible and -tolerant genotypes, were transformed with SACMV infectious clones and/or a CRISPR-editing construct targeting the MeE3L using PEG4000-mediated transfection. DNA and RNA were extracted from transformed protoplasts at 24 h post-transfection. Relative SACMV DNA accumulation was determined via qPCR using DpnI-digested total DNA, MeE3L relative expression was determined via reverse transcriptase qPCR, and results were analysed using one-way ANOVA, Tukey’s HSD test and the 2−ΔΔCTstatistical method. The MeE3L exonic region was sequenced on the ABI 3500XL Genetic Analyzer platform; and sequences were analysed for mutations using MAFTT and MEGA-X software. Construction of a phylogenetic tree was done using the Maximum Likelihood method and Jones-Taylor-Thornton (JTT) matrix-based model. Results The differential expression of unedited and mutant MeE3L during SACMV infection of model, susceptible and tolerant cassava protoplasts was determined within 7 weeks after commencement of tissue culture. The study also revealed that SACMV DNA accumulation in cassava protoplasts is genotype-dependent and induces multiple mutations in the tolerant landrace MeE3L homolog. Notably, the susceptible cassava landrace encodes a RINGless MeE3Lwhich is silenced by SACMV-induced mutations. SACMV also induces mutations which silence the MeE3L RING domain in protoplasts from and tolerant cassava landraces. Conclusions This protocol presented here halves the turnaround time for high-throughput screening of genes associated with the host response to SACMV. It provides evidence that a cassava E3 ligase is associated with the response to SACMV and forms a basis for validation of these findings by in planta functional and interaction studies.
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Affiliation(s)
- Patience Chatukuta
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Marie Emma Christine Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa.
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Harnessing High-throughput Phenotyping and Genotyping for Enhanced Drought Tolerance in Crop Plants. J Biotechnol 2020; 324:248-260. [PMID: 33186658 DOI: 10.1016/j.jbiotec.2020.11.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/28/2020] [Accepted: 11/08/2020] [Indexed: 12/17/2022]
Abstract
Development of drought-tolerant cultivars is one of the challenging tasks for the plant breeders due to its complex inheritance and polygenic regulation. Evaluating genetic material for drought tolerance is a complex process due to its spatiotemporal interactions with environmental factors. The conventional breeding approaches are costly, lengthy, and inefficient to achieve the expected gain in drought tolerance. In this regard, genomics-assisted breeding (GAB) offers promise to develop cultivars with improved drought tolerance in a more efficient, quicker, and cost-effective manner. The success of GAB depends upon the precision in marker-trait association and estimation of genomic estimated breeding values (GEBVs), which mostly depends on coverage and precision of genotyping and phenotyping. A wide gap between the discovery and practical use of quantitative trait loci (QTL) for crop improvement has been observed for many important agronomical traits. Such a limitation could be due to the low accuracy in QTL detection, mainly resulting from low marker density and manually collected phenotypes of complex agronomic traits. Increasing marker density using the high-throughput genotyping (HTG), and accurate and precise phenotyping using high-throughput digital phenotyping (HTP) platforms can improve the precision and power of QTL detection. Therefore, both HTG and HTP can enhance the practical utility of GAB along with a faster characterization of germplasm and breeding material. In the present review, we discussed how the recent innovations in HTG and HTP would assist in the breeding of improved drought-tolerant varieties. We have also discussed strategies, tools, and analytical advances made on the HTG and HTP along with their pros and cons.
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Jiwuba L, Danquah A, Asante I, Blay E, Onyeka J, Danquah E, Egesi C. Genotype by Environment Interaction on Resistance to Cassava Green Mite Associated Traits and Effects on Yield Performance of Cassava Genotypes in Nigeria. FRONTIERS IN PLANT SCIENCE 2020; 11:572200. [PMID: 33013995 PMCID: PMC7498573 DOI: 10.3389/fpls.2020.572200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/14/2020] [Indexed: 05/30/2023]
Abstract
Cassava is the main source of carbohydrate for over 70% of the people in Nigeria, the world's largest producer and consumer of the crop. The yields of cassava are, however, relatively low in Nigeria largely due to pests and disease infections that significantly lead to inconsistencies in productivity of cassava genotypes in various environments. Fifty-eight F1 hybrid cassava genotypes plus their two parents which served as check varieties were evaluated in three locations for two years (that is six environments). The objectives of the study were to evaluate genotype by environment interactions (GEI) on resistance to cassava green mite [CGM, Mononychellus tanajoa (Bondar)] associated traits and effects on yield performance of cassava genotypes in Nigeria and to identify superior genotypes that exhibit high stability which combine CGM resistance and high fresh root yield with general and specific environmental adaptation using additive main effects and multiplicative interaction (AMMI) and genotype stability index (GSI). The combined analysis of variance based on AMMI revealed significant genotype, environment, and genotype by environment interactions (GEI) for all traits. The percentage variation due to environment was higher than the percentage variation due to genotype for cassava green mite severity (CGMS), leaf retention (LR), root dry matter content (RDMC), and fresh root yield (FRY) indicating that environment greatly influenced the expression of these traits. The percentage variation due to GEI accounted for higher percentage variation than that of genotype and environment separately for all traits, indicating the influence of genotype by environment interaction on expression of the traits. These findings reveal that screening/evaluating for these traits needs multi-environment trials. According to GSI ranking, genotypes G31 (IBA131794), G19 (IBA131762), the check variety G52 (TMEB778), and G11 (IBA131748) were identified as the most stable and most resistant to CGM which also combine high FRY and other useful agronomic traits, implying that these traits in cassava can even be incorporated as preferred by farmers. These genotypes can be tested in more environments to determine their adaptability and potential recommendation for release to farmers for growing.
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Affiliation(s)
- Lydia Jiwuba
- Biotechnology Programme, National Root Crops Research Institute, NRCRI, Umudike, Nigeria
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Agyemang Danquah
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
- Department of Crop Science, University of Ghana, Accra, Ghana
| | - Isaac Asante
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
- Department of Plant and Environmental Biology, University of Ghana, Accra, Ghana
| | - Essie Blay
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
- Department of Crop Science, University of Ghana, Accra, Ghana
| | - Joseph Onyeka
- Biotechnology Programme, National Root Crops Research Institute, NRCRI, Umudike, Nigeria
| | - Eric Danquah
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
- Department of Crop Science, University of Ghana, Accra, Ghana
| | - Chiedozie Egesi
- Biotechnology Programme, National Root Crops Research Institute, NRCRI, Umudike, Nigeria
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
- Cassava Breeding Unit, International Institute for Tropical Agriculture (IITA), Ibadan, Nigeria
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Lentini Z, Restrepo G, Buitrago ME, Tabares E. Protocol for Rescuing Young Cassava Embryos. FRONTIERS IN PLANT SCIENCE 2020; 11:522. [PMID: 32457774 PMCID: PMC7227409 DOI: 10.3389/fpls.2020.00522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/06/2020] [Indexed: 05/13/2023]
Abstract
Embryo rescue (ER) in cassava breeding has several relevant applications, from the recovery of broad crosses to the recovery of seeds from the standard pollination program. Cassava fruit setting may drop from 100%, during the 1st week after pollination, to less than 40% during the 2nd week after pollination due to the abscission of fruits depending on genotypes. Therefore, the availability of an ER protocol for early stages of embryo development, in particular during the first 2 weeks after pollination (prior the cotyledonary stage), could have practical implications for cassava breeding. Until now, attempts to recover cassava immature embryos at stages of development earlier than the cotyledonary stage failed. The earliest successful rescue reported in cassava is from embryos excised 32-36 days after anthesis (DAA). However, limited information was available regarding embryo development in cassava. This work studied and documented the stage of embryo development in histological sections of hand-pollinated ovules fixed from 1 to 30 days after anthesis (DAA). At 7 DAA, zygotes were just at the first stages of cell division (pro- embryo stage). At 14 DAA, embryos were at the pre-globular stage. Embryos at the early globular stage were observed in sections fixed at 21 DAA, and at the proper globular stage at 24 DAA. Samples at 30 DAA contained cotyledonary embryos that easily developed after ovule culture into viable plants using existing protocols. A second contribution of this work is the development of a protocol for the recovery of fully developed plants from immature embryos rescued and cultured in vitro as early as 7-14 DAA. Since embryos collected at this age are at the pro-embryo to pre-globular stage, ovary/ovule culture was necessary. A method is described whereby ovules were cultured to allow the development of pro-embryos and pre-globular stage embryos into the cotyledonary stage. Subsequently, these mature embryos were excised from the ovules to induce germination and the recovery of fully developed plants.
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Affiliation(s)
- Zaida Lentini
- Center of Specialized Natural and Biotechnological Ingredients (CINEB), School of Natural Sciences, Universidad Icesi, Cali, Colombia
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Lentini Z, González Á, Tabares E, Buitrago ME, Wêdzony M. Studies on Gynogenesis Induction in Cassava ( Manihot esculenta Crantz) Unpollinated Ovule Culture. FRONTIERS IN PLANT SCIENCE 2020; 11:365. [PMID: 32318083 PMCID: PMC7147354 DOI: 10.3389/fpls.2020.00365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/13/2020] [Indexed: 05/24/2023]
Abstract
Cassava (Manihot esculenta Crantz) is an important crop for subsistence farming in tropical and subtropical regions. There is a need to increase the rate of genetic gain to develop varieties adapted to new environmental conditions affected by climate change, which also influences the patterns of pests and diseases. The rate of cassava genetic improvement is limited by the difficulty in obtaining true-breeding types (inbred/homozygous lines). Cassava inbreeding obtained through conventional sequential self-pollination increases exposure of useful recessive traits and breeding value of progenitors. However, it takes 10-15 years to produce homozygous lines through successive self-pollination. Doubled haploid (DH) technology is a functional alternative to progressive self-pollination, and is already widely used in major crops to accelerate inbreeding. This work aimed at developing a protocol for the culture of isolated ovules and the induction of gynogenesis in cassava. Basic groundbreaking studies on cassava embryo sac development are presented. A protocol using unpollinated ovules collected from ovaries 1 day after anthesis is described. In the unpollinated-cultured ovules, the presence of embryos formed probably from the egg cells and not surrounded by the endosperm, was documented by anatomical analyses. This achievement is an important first step in the development of a reproducible gynogenesis protocol for the generation of doubled haploids in cassava. This protocol can also be useful as a starting point to obtain DHs using alternative methods of induction such as pollination of cassava with pollen of distant species or with cassava pollen irradiated with gamma rays.
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Affiliation(s)
- Zaida Lentini
- Center of Specialized Natural and Biotechnological Ingredients (CINEB), School of Natural Sciences, Universidad Icesi, Cali, Colombia
| | - Álfora González
- School of Natural Sciences, Universidad Icesi, Cali, Colombia
| | - Eddie Tabares
- School of Natural Sciences, Universidad Icesi, Cali, Colombia
| | - María E. Buitrago
- Center of Specialized Natural and Biotechnological Ingredients (CINEB), School of Natural Sciences, Universidad Icesi, Cali, Colombia
| | - Maria Wêdzony
- Institute of Biology, Pedagogical University of Cracow, Kraków, Poland
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Malik AI, Kongsil P, Nguyễn VA, Ou W, Sholihin, Srean P, Sheela MN, Becerra López-Lavalle LA, Utsumi Y, Lu C, Kittipadakul P, Nguyễn HH, Ceballos H, Nguyễn TH, Selvaraj Gomez M, Aiemnaka P, Labarta R, Chen S, Amawan S, Sok S, Youabee L, Seki M, Tokunaga H, Wang W, Li K, Nguyễn HA, Nguyễn VĐ, Hàm LH, Ishitani M. Cassava breeding and agronomy in Asia: 50 years of history and future directions. BREEDING SCIENCE 2020; 70:145-166. [PMID: 32523397 PMCID: PMC7272245 DOI: 10.1270/jsbbs.18180] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 09/29/2019] [Indexed: 09/29/2023]
Abstract
In Asia, cassava (Manihot esculenta) is cultivated by more than 8 million farmers, driving the rural economy of many countries. The International Center for Tropical Agriculture (CIAT), in partnership with national agricultural research institutes (NARIs), instigated breeding and agronomic research in Asia, 1983. The breeding program has successfully released high-yielding cultivars resulting in an average yield increase from 13.0 t ha-1 in 1996 to 21.3 t ha-1 in 2016, with significant economic benefits. Following the success in increasing yields, cassava breeding has turned its focus to higher-value traits, such as waxy cassava, to reach new market niches. More recently, building resistance to invasive pests and diseases has become a top priority due to the emergent threat of cassava mosaic disease (CMD). The agronomic research involves driving profitability with advanced technologies focusing on better agronomic management practices thereby maintaining sustainable production systems. Remote sensing technologies are being tested for trait discovery and large-scale field evaluation of cassava. In summary, cassava breeding in Asia is driven by a combination of food and market demand with technological innovations to increase the productivity. Further, exploration in the potential of data-driven agriculture is needed to empower researchers and producers for sustainable advancement.
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Affiliation(s)
- Al Imran Malik
- International Center for Tropical Agriculture (CIAT-Laos), Lao PDR Office, Dong Dok, Ban Nongviengkham, Vientiane, Lao PDR
| | - Pasajee Kongsil
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Vũ Anh Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Wenjun Ou
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Sholihin
- Indonesian Legume and Tuber Crops Research Institute, Kendalpayak Km 8, PO BOX 66, Malang 65101, Indonesia
| | - Pao Srean
- Faculty of Agriculture & Food Processing, University of Battambang, Battambang, Cambodia
| | - MN Sheela
- Central Tuber Crops Research Institute Sreekariyam, Thiruvananthapuram-605 017, Kerala, India
| | | | - Yoshinori Utsumi
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Cheng Lu
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Piya Kittipadakul
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Hữu Hỷ Nguyễn
- Hung Loc Agricultural Research Center, Institute for Agriculture in Southern Vietnam, 121 Nguyen Binh Khiem, District 1, HCM City, Vietnam
| | - Hernan Ceballos
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Trọng Hiển Nguyễn
- Root and Tuber Crop Research and Development Center, Food and Field Crop Research Institute, Vinh Quynh, Thanh Tri, Hanoi, Vietnam
| | - Michael Selvaraj Gomez
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Pornsak Aiemnaka
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Ricardo Labarta
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Songbi Chen
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Suwaluk Amawan
- Rayong Field Crops Research Center, Sukumvit Rd, Huaypong, Meang, Rayong 21150, Thailand
| | - Sophearith Sok
- International Center for Tropical Agriculture (CIAT-Asia), Phnom Penh, Cambodia
| | - Laothao Youabee
- International Center for Tropical Agriculture (CIAT-Laos), Lao PDR Office, Dong Dok, Ban Nongviengkham, Vientiane, Lao PDR
| | - Motoaki Seki
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroki Tokunaga
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Wenquan Wang
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Kaimian Li
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Hai Anh Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Văn Đồng Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Lê Huy Hàm
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Manabu Ishitani
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
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de Oliveira EJ, de Oliveira SAS, Otto C, Alicai T, de Freitas JPX, Cortes DFM, Pariyo A, Liri C, Adiga G, Balmer A, Klauser D, Robinson M. A novel seed treatment-based multiplication approach for cassava planting material. PLoS One 2020; 15:e0229943. [PMID: 32142527 PMCID: PMC7059944 DOI: 10.1371/journal.pone.0229943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 02/18/2020] [Indexed: 11/18/2022] Open
Abstract
Cassava (Manihot esculenta Crantz) is an important food security crop in many parts of the developing world. The crop's high yield potential and multitude of uses-both for nutrition and processing-render cassava a promising driver for the development of rural value chains. It is traditionally propagated from stem cuttings of up to 30 cm in length, giving a multiplication rate as low as 1:10. Propagating cassava traditionally is very inefficient, which leads to challenges in the production and distribution of quality planting material and improved cultivars, greatly limiting the impact of investments in crop breeding. The work described in the present study aimed to develop a seed treatment approach to facilitate the use of shorter seed pieces, increasing the multiplication rate of cassava and thus making the crop's seed systems more efficient. After several tests, formulation was identified, consisting of thiamethoxam 21 g ha-1, mefenoxam 1.0 g ha-1, fludioxonil 1.3 g ha-1, thiabendazole 7.5 g ha-1 and Latex 2% as a binder. Plant growing from seed pieces treated with this formulation displayed increased crop establishment and early crop vigor, leading to an improved productivity throughout a full growing cycle. This allowed to reduce the cassava seed piece size to 8 cm with no negative effects on germination and crop establishment, leading to yields comparable to those from untreated 16 cm pieces. This, in turn, will allow to increase the multiplication ratio of cassava by a factor of up to 3. Notably, this was possible under regular field conditions and independently of any specialised treatment facilities. Compared with existing seed production protocols, the increased multiplication rates allowed for efficiency gains of between 1 to 1.9 years compared to conventional five-year cycles. We believe that the technology described here holds considerable promise for developing more reliable and remunerative delivery channels for quality cassava planting material and improved genetics.
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Affiliation(s)
| | | | - Caroline Otto
- Syngenta Foundation for Sustainable Agriculture, Basel, Switzerland
| | - Titus Alicai
- National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | | | | | - Anthony Pariyo
- National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | - Charles Liri
- National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | - Gerald Adiga
- National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | - Andrea Balmer
- Syngenta Foundation for Sustainable Agriculture, Basel, Switzerland
| | - Dominik Klauser
- Syngenta Foundation for Sustainable Agriculture, Basel, Switzerland
| | - Mike Robinson
- Syngenta Foundation for Sustainable Agriculture, Basel, Switzerland
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Pineda M, Yu B, Tian Y, Morante N, Salazar S, Hyde PT, Setter TL, Ceballos H. Effect of Pruning Young Branches on Fruit and Seed Set in Cassava. FRONTIERS IN PLANT SCIENCE 2020; 11:1107. [PMID: 32793264 PMCID: PMC7390943 DOI: 10.3389/fpls.2020.01107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 07/06/2020] [Indexed: 05/13/2023]
Abstract
Flowering in cassava is closely linked with branching. Early-flowering genotypes branch low and abundantly. Although farmers prefer late flowering genotypes because of their erect plant architecture, their usefulness as progenitors in breeding is limited by their low seed production. In general, the first inflorescence aborts in cassava. Preventing this abortion would result in early production of seeds and make cassava breeding more efficient. The objective of this study was to assess if pruning young branches prevents the abortion of first inflorescences and promotes early fruit and seed set. Four genotypes with early, late, very late, and no flowering habits were grown under an extended photoperiod (EP) or normal dark night conditions (DN). Additional treatments included pruning young branches at the first or second flowering event and spraying (or not) benzyladenine (BA) after pruning. One genotype failed to flower and was not considered further. For the remaining genotypes, EP proved crucial to induce an earlier flowering, which is a pre-requisite for pruning. Total production of seeds in EP plots was 2,971 versus 150 in DN plots. For plants grown under EP, the average number of seeds per plant without pruning was 3.88, whereas those pruned produced 17.60 seeds per plant. Pruning at the first branching event led to higher number of seeds per plant (26.25) than pruning at the second flowering event (8.95). In general, applying BA was beneficial (38.52 and 13.98 seeds/plant with or without spraying it, respectively). The best combination of treatments was different for each genotype. Pruning young branches and applying BA in the first flowering event not only prevented the abortion of inflorescences but also induced the feminization of male flowers into hermaphrodite or female-only flowers. The procedures suggested from this study (combining EP, pruning young branches, and spraying BA), allowed the production of a high number of seeds from erect cassava genotypes in a short period. The implementation of these procedures will improve the breeding efficiency in cassava.
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Affiliation(s)
- Marcela Pineda
- CGIAR Research Program on Roots Tubers and Bananas (RTB), The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Benchi Yu
- Cassava Program, Guangxi Subtropical Crops Research Institute, Nanning, China
| | - Yinong Tian
- Cassava Program, Guangxi Subtropical Crops Research Institute, Nanning, China
| | - Nelson Morante
- CGIAR Research Program on Roots Tubers and Bananas (RTB), The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Sandra Salazar
- CGIAR Research Program on Roots Tubers and Bananas (RTB), The Alliance of Bioversity International and the 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
| | - Hernán Ceballos
- CGIAR Research Program on Roots Tubers and Bananas (RTB), The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
- *Correspondence: Hernán Ceballos,
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de Andrade LRB, Sousa MBE, Oliveira EJ, de Resende MDV, Azevedo CF. Cassava yield traits predicted by genomic selection methods. PLoS One 2019; 14:e0224920. [PMID: 31725759 PMCID: PMC6855463 DOI: 10.1371/journal.pone.0224920] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/24/2019] [Indexed: 01/01/2023] Open
Abstract
Genomic selection (GS) has been used to optimize genetic gains when phenotypic selection is considered costly and difficult to measure. The objective of this work was to evaluate the efficiency and consistency of GS prediction for cassava yield traits (Manihot esculenta Crantz) using different methods, taking into account the effect of population structure. BLUPs and deregressed BLUPs were obtained for 888 cassava accessions and evaluated for fresh root yield, dry root yield and dry matter content in roots in 21 trials conducted from 2011 to 2016. The deregressed BLUPs obtained for the accessions from a 48K single nucleotide polymorphism dataset were used for genomic predictions based on the BayesB, BLASSO, RR-BLUP, G-BLUP and RKHS methods. The accessions’ BLUPs were used in the validation step using four cross-validation strategies, taking into account population structure and different GS methods. Similar estimates of predictive ability and bias were identified for the different genomic selection methods in the first cross-validation strategy. Lower predictive ability was observed for fresh root yield (0.4569 –RR-BLUP to 0.4756—RKHS) and dry root yield (0.4689 –G-BLUP to 0.4818—RKHS) in comparison with dry matter content (0.5655 –BLASSO to 0.5670 –RKHS). However, the RKHS method exhibited higher efficiency and consistency in most of the validation scenarios in terms of prediction ability for fresh root yield and dry root yield. The correlations of the genomic estimated breeding values between the genomic selection methods were quite high (0.99–1.00), resulting in high coincidence of clone selection regardless of the genomic selection method. The deviance analyses within and between the validation clusters formed by the discriminant analysis of principal components were significant for all traits. Therefore, this study indicated that i) the prediction of dry matter content was more accurate compared to that of yield traits, possibly as a result of the smaller influence of non-additive genetic effects; ii) the RKHS method resulted in high and stable prediction ability in most of the validation scenarios; and iii) some kinship between the validation and training populations is desirable in order for genomic selection to succeed due to the significant effect of population structure on genomic selection predictions.
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Affiliation(s)
| | - Massaine Bandeira e Sousa
- Center of Agrarian, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Bahia, Brazil
| | | | - Marcos Deon Vilela de Resende
- Department of Forestry Engineering, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Embrapa Florestas, Colombo, Paraná, Brazil
- Department of Statistics, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Hyde PT, Guan X, Abreu V, Setter TL. The anti-ethylene growth regulator silver thiosulfate (STS) increases flower production and longevity in cassava ( Manihot esculenta Crantz). PLANT GROWTH REGULATION 2019; 90:441-453. [PMID: 32214568 PMCID: PMC7081664 DOI: 10.1007/s10725-019-00542-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 09/17/2019] [Indexed: 05/26/2023]
Abstract
Cassava, which produces edible starchy roots, is an important staple food for hundreds of millions of people in the tropics. Breeding of cassava is hampered by its poor flower production, flower abortion, and lack of reproductive prolificacy. The current work determined that ethylene signalling affects floral development in cassava and that the anti-ethylene plant growth regulator silver thiosulfate (STS) mitigates the effects of ethylene on flower development. STS did not affect the timing of flower initiation, but improved early inflorescence and flower development as well as flower longevity such that flower numbers were increased. STS did not affect shoot and storage root growth. Studies of silver accumulation and treatment localization support the hypothesis that the beneficial effects of STS are confined to tissues of the shoot apex. The most effective timing of application was before inflorescence appearance extending to post-flower appearance. Based on this work a recommended protocol for STS use was developed. This work has the potential to improve methods for enhancing cassava flower development in breeding nurseries and thereby synchronize flowering of desired parents and enable the production of abundant progeny of desired crosses.
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Affiliation(s)
- Peter T. Hyde
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, 517 Bradfield Hall, Ithaca, NY USA
| | - Xian Guan
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, 517 Bradfield Hall, Ithaca, NY USA
| | - Viviane Abreu
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, 517 Bradfield Hall, Ithaca, NY USA
| | - Tim L. Setter
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, 517 Bradfield Hall, Ithaca, NY USA
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Genomic selection for productive traits in biparental cassava breeding populations. PLoS One 2019; 14:e0220245. [PMID: 31344109 PMCID: PMC6658084 DOI: 10.1371/journal.pone.0220245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/11/2019] [Indexed: 11/19/2022] Open
Abstract
Cassava improvement using traditional breeding strategies is slow due to the species’ long breeding cycle. However, the use of genomic selection can lead to a shorter breeding cycle. This study aimed to estimate genetic parameters for productive traits based on pedigree (pedigree and phenotypic information) and genomic (markers and phenotypic information) analyses using biparental crosses at different stages of selection. A total of 290 clones were genotyped and phenotyped for fresh root yield (FRY), dry matter content (DMC), dry yield (DY), fresh shoot yield (FSY) and harvest index (HI). The clones were evaluated in clonal evaluation trials (CET), preliminary yield trials (PYT), advanced yield trials (AYT) and uniform yield trials (UYT), from 2013 to 2018 in ten locations. The breeding stages were analyzed as follows: one stage (CET), two stages (CET and PYT), three stages (CET, PYT and AYT) and four stages (CET, PYT, AYT and UYT). The genomic predictions were analyzed via k-fold cross-validation based on the genomic best linear unbiased prediction (GBLUP) considering a model with genetic additive effects and genotype × location interactions. Genomic and pedigree accuracies were moderate to high (0.56–0.72 and 0.62–0.78, respectively) for important starch-related traits such as DY and FRY; when considering one breeding stage (CET) with the aim of early selection, the genomic accuracies ranged from 0.60 (DMC) to 0.71 (HI). Moreover, the correlations between the genomic estimation breeding values of one-stage genomic analysis and the estimated breeding values of the four-stage (full data set) pedigree analysis were high for all traits as well as for a selection index including all traits. The results indicate great possibilities for genomic selection in cassava, especially for selection early in the breeding cycle (saving time and effort).
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Ramos Abril LN, Pineda LM, Wasek I, Wedzony M, Ceballos H. Reproductive biology in cassava: stigma receptivity and pollen tube growth. Commun Integr Biol 2019; 12:96-111. [PMID: 31308874 PMCID: PMC6615524 DOI: 10.1080/19420889.2019.1631110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/31/2019] [Accepted: 06/06/2019] [Indexed: 11/18/2022] Open
Abstract
Knowledge on the reproductive biology of cassava, relevant to breeders and molecular geneticists, is still limited. Therefore, different studies were carried out to determine the duration of stigma receptivity and the rate of pollen tube growth. Inflorescences were covered for up to 3 days after the first opening of the bracts (e.g. anthesis day) to prevent open pollination. Results indicate that fruit and seed set are drastically reduced when flowers were covered for 2 or 3 days. However, fruits and seeds were obtained even from flowers that had been covered for 3 days after anthesis, although at low frequency. The rate of pollen tube growth was assessed in many combinations of female and male progenitors crossed through controlled pollinations and collecting the pistils at varying hours after pollination (HAP). Pollen tube growth is fast during the first 6 HAP reaching the tip of the nucellar beak. The growth slows down thereafter, taking 10 additional hours to reach the end of the beak. The growth of pollen tubes slows down even further until they enter the embryo sac. Only 10% of samples showed pollen tubes entering the embryo sac between 48 and 66 HAP. Although several tubes may reach the nucellar beak, only one was observed entering the embryo sac. Results, across the different experiments, were highly variable suggesting that the timeline of fertilization is influenced both by genotypic and environmental factors as well as the manual manipulation of inflorescences and cyathia.
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Affiliation(s)
- L N Ramos Abril
- Cassava Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia.,Universidad Nacional de Colombia, Palmira, Colombia
| | - L M Pineda
- Cassava Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - I Wasek
- Pedagogical University, Cracow, Poland
| | - M Wedzony
- Pedagogical University, Cracow, Poland
| | - H Ceballos
- Cassava Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Adeyemo OS, Hyde PT, Setter TL. Identification of FT family genes that respond to photoperiod, temperature and genotype in relation to flowering in cassava (Manihot esculenta, Crantz). PLANT REPRODUCTION 2019; 32:181-191. [PMID: 30543044 PMCID: PMC6500508 DOI: 10.1007/s00497-018-00354-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/03/2018] [Indexed: 05/26/2023]
Abstract
Cassava is a starch-storing root crop that is an important source of dietary energy in tropical regions of the world. Genetic improvement of cassava by breeding is hindered by late flowering and sparse flower production in lines that are needed as parents. To advance understanding of regulatory mechanisms in cassava, this work sought to identify and characterize homologs of the FLOWERING LOCUS T (FT) gene. Ten members of the phosphatidylethanolamine-binding protein gene family, to which FT belongs, were obtained from the cassava genome database. Phylogenetic and sequence analysis of these proteins was used to identify two putative FT homologs which had amino acid sequences at key positions in accordance with those predicted for functional FTs. Expression of these ten genes was determined in mature leaves, immature leaves, flower buds, fibrous roots, storage roots and stem. The FT transcripts were expressed in mature leaves, as expected for their possible role in leaf-to-apical meristem signaling. In growth chamber studies, plants flowered earlier in long-day photoperiod than in short-day photoperiod. Expression studies indicated that while MeFT1 was expressed in leaves without a clear-cut photoperiod response, MeFT2 was expressed in a photoperiod-dependent manner, consistent with its involvement in photoperiodic control of flowering. In growth chambers that subjected plants to a range of temperatures from 22 to 34 °C, flowering was delayed by warmer temperatures although MeFT1 and MeFT2 expression declined in only one genotype, indicating other factors regulate this response. The earliest flowering genotype, IBA980002, had high levels of MeFT1 and MeFT2 expression, suggesting that both homologs contribute to earliness of this genotype.
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Affiliation(s)
- Oluwabusayo Sarah Adeyemo
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Peter T Hyde
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Tim L Setter
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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Li M, Yang S, Xu W, Pu Z, Feng J, Wang Z, Zhang C, Peng M, Du C, Lin F, Wei C, Qiao S, Zou H, Zhang L, Li Y, Yang H, Liao A, Song W, Zhang Z, Li J, Wang K, Zhang Y, Lin H, Zhang J, Tan W. The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development. BMC PLANT BIOLOGY 2019; 19:119. [PMID: 30935381 PMCID: PMC6444543 DOI: 10.1186/s12870-019-1708-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 03/11/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. RESULTS Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. CONCLUSIONS We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.
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Affiliation(s)
- Ming Li
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Songtao Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Wei Xu
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Zhigang Pu
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Junyan Feng
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Zhangying Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong People’s Republic of China
| | - Cong Zhang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Meifang Peng
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Chunguang Du
- Department of Biology, Montclair State University, Montclair, NJ 07043 USA
| | - Feng Lin
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061 Sichuan People’s Republic of China
| | - Changhe Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Shuai Qiao
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Hongda Zou
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong People’s Republic of China
| | - Lei Zhang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Yan Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Huan Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Anzhong Liao
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Wei Song
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
| | - Zhongren Zhang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Ji Li
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Kai Wang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Yizheng Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan People’s Republic of China
| | - Jinbo Zhang
- Novogene Bioinformatics Institute, Beijing, 100083 People’s Republic of China
| | - Wenfang Tan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 Sichuan People’s Republic of China
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OLIVEIRA PAULOHENRIQUEGDE, BARBOSA ANACLAUDIAO, DINIZ RAFAELP, OLIVEIRA EDERJDE, FERREIRA CLAUDIAF. Molecular marker assisted selection for increasing inbreeding in S1 populations of cassava. AN ACAD BRAS CIENC 2018; 90:3853-3869. [PMID: 30427393 DOI: 10.1590/0001-3765201820180278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/02/2018] [Indexed: 01/15/2023] Open
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45
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Delaquis E, Andersen KF, Minato N, Cu TTL, Karssenberg ME, Sok S, Wyckhuys KAG, Newby JC, Burra DD, Srean P, Phirun I, Le ND, Pham NT, Garrett KA, Almekinders CJM, Struik PC, de Haan S. Raising the Stakes: Cassava Seed Networks at Multiple Scales in Cambodia and Vietnam. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00073] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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46
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Nduwumuremyi A, Melis R, Shanahan P, Theodore A. Genetic inheritance of pulp colour and selected traits of cassava (Manihot esculenta Crantz) at early generation selection. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:3190-3197. [PMID: 29230819 DOI: 10.1002/jsfa.8825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 12/01/2017] [Accepted: 12/06/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The early generation selection of cassava quantitative and qualitative traits saves breeding resources as it can shorten breeding schemes. Inheritance analysis provides important breeding information for developing new improved varieties. This study aimed at developing an F1 segregating cassava population and determining mode of gene action of pulp colour and selected traits at early generation selection (F1 seedling and clones). RESULTS The 15 families exhibited significant (P < 0.05) phenotypic variation between offspring. The general combining ability (GCA) was significant for all traits except cassava brown streak disease on leaves, whereas specific combining ability (SCA) was significant for all evaluated traits. The Garukansubire and Gitamisi genotypes were the best general combiners for improving fresh storage root yield, while G1 and G2 were the best general combiners for improved carotenoid (yellow/orange pulp colour) and delayed physiological postharvest deterioration. The pulp colour had the highest GCA/SCA ratio and percent sum of squares due to GCA. CONCLUSION The 15 F1 families exhibited essential genetic diversity for cassava improvement. The expression of most cassava traits was controlled by both additive and non-additive gene action. The study elucidated the role of dominance effects over the additive effects for the evaluated traits. However, the pulp colour was predominantly controlled by additive gene action. This implies the possibility of improving cassava through conventional breeding using recurrent selection for most traits. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Athanase Nduwumuremyi
- African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Scottville, South Africa
- Rwanda Agriculture Board (RAB), Kigali, Rwanda
| | - Rob Melis
- African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Scottville, South Africa
| | - Paul Shanahan
- African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Scottville, South Africa
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47
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Neves RJ, Diniz RP, Oliveira EJDE. Productive potential of cassava plants (Manihot esculenta Crantz) propagated by leaf buds. AN ACAD BRAS CIENC 2018; 90:1733-1747. [PMID: 29694501 DOI: 10.1590/0001-3765201820170867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/22/2017] [Indexed: 11/22/2022] Open
Abstract
New techniques of rapid multiplication of cassava (Manihot esculenta Crantz) have been developed, requiring technical support for large-scale use. This work main to evaluate the agronomic performance of plantlets obtained by leaf buds technique against stem cuttings in the field conditions. The work was conducted using the randomized block design in a factorial scheme with 3 varieties (BRS Kiriris, 98150-06, 9624-09) × 4 origins of the plantlets (conventional - stem cuttings of 20 cm length, leaf buds of the upper, middle and inferior stem part) × 2 agrochemicals (control and treated). There was a remarkable decrease in some agronomic traits that ranged from 23% (number of branches) to 62% (shoot weight) when using leaf buds plantlets. The treatment of plantlets with agrochemicals promoted significant increases in all traits, ranging from 26% (number of roots per plant) to 46% (shoot weight). The plantlets originating from leaf buds of the upper and middle parts were able to generate stem-like plants similar to stem-derived ones. Despite its lower agronomic performance under field conditions, multiplication by leaf buds may generate five times the number of propagules in comparison with the conventional multiplication, and therefore it could be a viable alternative for rapid cassava multiplication.
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Affiliation(s)
- Reizaluamar J Neves
- Centro de Ciências Agrárias, Ambientais e Biológicas, Universidade Federal do Recôncavo da Bahia, Rua Rui Barbosa, 710, 44380-000 Cruz das Almas, BA, Brazil
| | - Rafael P Diniz
- Centro de Ciências Agrárias, Ambientais e Biológicas, Universidade Federal do Recôncavo da Bahia, Rua Rui Barbosa, 710, 44380-000 Cruz das Almas, BA, Brazil.,Embrapa Mandioca e Fruticultura, Rua da Embrapa, s/n, Caixa Postal 007, 44380-000 Cruz das Almas, BA, Brazil
| | - Eder J DE Oliveira
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, s/n, Caixa Postal 007, 44380-000 Cruz das Almas, BA, Brazil
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Piaskowski J, Hardner C, Cai L, Zhao Y, Iezzoni A, Peace C. Genomic heritability estimates in sweet cherry reveal non-additive genetic variance is relevant for industry-prioritized traits. BMC Genet 2018; 19:23. [PMID: 29636022 PMCID: PMC5894190 DOI: 10.1186/s12863-018-0609-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/22/2018] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Sweet cherry is consumed widely across the world and provides substantial economic benefits in regions where it is grown. While cherry breeding has been conducted in the Pacific Northwest for over half a century, little is known about the genetic architecture of important traits. We used a genome-enabled mixed model to predict the genetic performance of 505 individuals for 32 phenological, disease response and fruit quality traits evaluated in the RosBREED sweet cherry crop data set. Genome-wide predictions were estimated using a repeated measures model for phenotypic data across 3 years, incorporating additive, dominance and epistatic variance components. Genomic relationship matrices were constructed with high-density SNP data and were used to estimate relatedness and account for incomplete replication across years. RESULTS High broad-sense heritabilities of 0.83, 0.77, and 0.76 were observed for days to maturity, firmness, and fruit weight, respectively. Epistatic variance exceeded 40% of the total genetic variance for maturing timing, firmness and powdery mildew response. Dominance variance was the largest for fruit weight and fruit size at 34% and 27%, respectively. Omission of non-additive sources of genetic variance from the genetic model resulted in inflation of narrow-sense heritability but minimally influenced prediction accuracy of genetic values in validation. Predicted genetic rankings of individuals from single-year models were inconsistent across years, likely due to incomplete sampling of the population genetic variance. CONCLUSIONS Predicted breeding values and genetic values revealed many high-performing individuals for use as parents and the most promising selections to advance for cultivar release consideration, respectively. This study highlights the importance of using the appropriate genetic model for calculating breeding values to avoid inflation of expected parental contribution to genetic gain. The genomic predictions obtained will enable breeders to efficiently leverage the genetic potential of North American sweet cherry germplasm by identifying high quality individuals more rapidly than with phenotypic data alone.
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Affiliation(s)
- Julia Piaskowski
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Craig Hardner
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation University of Queensland, Brisbane, Australia
| | - Lichun Cai
- Department of Horticulture, Michigan State University, East Lansing, MI 48824-1325 USA
| | - Yunyang Zhao
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081 USA
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, East Lansing, MI 48824-1325 USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
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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. THE 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] [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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50
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Ligaba-Osena A, Jones J, Donkor E, Chandrayan S, Pole F, Wu CH, Vieille C, Adams MWW, Hankoua BB. Novel Bioengineered Cassava Expressing an Archaeal Starch Degradation System and a Bacterial ADP-Glucose Pyrophosphorylase for Starch Self-Digestibility and Yield Increase. FRONTIERS IN PLANT SCIENCE 2018; 9:192. [PMID: 29541080 PMCID: PMC5836596 DOI: 10.3389/fpls.2018.00192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 02/01/2018] [Indexed: 11/06/2023]
Abstract
To address national and global low-carbon fuel targets, there is great interest in alternative plant species such as cassava (Manihot esculenta), which are high-yielding, resilient, and are easily converted to fuels using the existing technology. In this study the genes encoding hyperthermophilic archaeal starch-hydrolyzing enzymes, α-amylase and amylopullulanase from Pyrococcus furiosus and glucoamylase from Sulfolobus solfataricus, together with the gene encoding a modified ADP-glucose pyrophosphorylase (glgC) from Escherichia coli, were simultaneously expressed in cassava roots to enhance starch accumulation and its subsequent hydrolysis to sugar. A total of 13 multigene expressing transgenic lines were generated and characterized phenotypically and genotypically. Gene expression analysis using quantitative RT-PCR showed that the microbial genes are expressed in the transgenic roots. Multigene-expressing transgenic lines produced up to 60% more storage root yield than the non-transgenic control, likely due to glgC expression. Total protein extracted from the transgenic roots showed up to 10-fold higher starch-degrading activity in vitro than the protein extracted from the non-transgenic control. Interestingly, transgenic tubers released threefold more glucose than the non-transgenic control when incubated at 85°C for 21-h without exogenous application of thermostable enzymes, suggesting that the archaeal enzymes produced in planta maintain their activity and thermostability.
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Affiliation(s)
- Ayalew Ligaba-Osena
- College of Agriculture and Related Sciences, Delaware State University, Dover, DE, United States
| | - Jenna Jones
- College of Agriculture and Related Sciences, Delaware State University, Dover, DE, United States
| | - Emmanuel Donkor
- College of Agriculture and Related Sciences, Delaware State University, Dover, DE, United States
| | - Sanjeev Chandrayan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Farris Pole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Claire Vieille
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Bertrand B. Hankoua
- College of Agriculture and Related Sciences, Delaware State University, Dover, DE, United States
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