Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Identification of Genomic Regions Associated with Flowering Traits in Cassava (Manihot esculenta Crantz)

Julius K. Baguma
* ORCID logo ,
Ssettumba B. Mukasa
,
Ephraim Nuwamanya
,
Titus Alicai
ORCID logo ,
Christopher Abu Omongo
ORCID logo ,
Mildred Ochwo Ssemakula
,
Alfred Ozimati
ORCID logo ,
Williams Esuma
,
Michael Kanaabi
ORCID logo ,
Enoch Wembabazi
,
Yona Baguma
,
Robert Kawuki
Version 1 : Received: 1 December 2023 / Approved: 4 December 2023 / Online: 4 December 2023 (10:18:19 CET)

A peer-reviewed article of this Preprint also exists.

Baguma, J.K.; Mukasa, S.B.; Nuwamanya, E.; Alicai, T.; Omongo, C.A.; Ochwo-Ssemakula, M.; Ozimati, A.; Esuma, W.; Kanaabi, M.; Wembabazi, E.; Baguma, Y.; Kawuki, R.S. Identification of Genomic Regions for Traits Associated with Flowering in Cassava (Manihot esculenta Crantz). Plants 2024, 13, 796. Baguma, J.K.; Mukasa, S.B.; Nuwamanya, E.; Alicai, T.; Omongo, C.A.; Ochwo-Ssemakula, M.; Ozimati, A.; Esuma, W.; Kanaabi, M.; Wembabazi, E.; Baguma, Y.; Kawuki, R.S. Identification of Genomic Regions for Traits Associated with Flowering in Cassava (Manihot esculenta Crantz). Plants 2024, 13, 796.

Abstract

Flowering in cassava is crucial for generation of botanical seed for breeding. However, most farmer preferred genotypes are poor at flowering, exhibit great disparity in time and amount of flowering or never flower. To elucidate the genetic basis of such a flowering behaviour, 293 diverse cassava accessions were evaluated for flowering traits under two locations and seasons in Uganda. Genotyping by 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 (PC) and kinships showed clustering, the first five PCs accounted for 49.2% of the observed genetic variation. Linkage disequilibrium (LD) estimation was averagely 0.32 at a distance of ~2850kb (kilo base pairs). Polymorphism information content (PIC) and minor allele frequency (MAF) were 0.25 and 0.23, respectively. Genome-wide association study (GWAS) analysis uncovered 53 significant marker-trait associations (MTA) with flowering traits involving 27 loci. Two loci, SNPs S5_29309724 and S15_11747301 were associated with all the flowering traits. Using five of the 27 SNPs with Phenotype_Variance_Explained (PVE) ≥ 5%, 37 candidate genes were identified in the peak SNP sites located within 50kb upstream or downstream, most were 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 in cassava, the identified SNPs could be useful in marker-assisted selection to overcome hybridization challenges like unsynchronized flowering, and candidate gene validation.

Keywords

flowering traits; first branching; branching levels; flowering behaviour; functional annotations

Subject

Biology and Life Sciences, Plant Sciences

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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