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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) 2024; 13:796. [PMID: 38592820 PMCID: PMC10974989 DOI: 10.3390/plants13060796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [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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