Biology subjects

Olukolu, B. A.

Publications and source records attributed to Olukolu, B. A..

6 recordsLinked to original sources

bioRxiv2022

Diversity, Phylogenetic Relationships, And Expression Profiles Of Invertase Inhibitor Genes In Sweetpotato

Invertases and their inhibitor proteins are key regulators of carbon allocation in plants. Manipulation of invertase inhibitor (ITI) activity can potentially increase crop yield. The aim of this study was to determine the sequence diversity, phylogenetic relationships, and expression profiles of ITI genes in sweetpotato(Ipomoea batatas).. The coding sequences of two ITI paralogs (SPITI1 and SPITI2) were cloned from two sweetpotato varieties (Beauregard and Jewel) and sequenced. The DNA sequences were used to deduce amino acids sequences and predicted protein properties. Quantitative PCR (qPCR) was carried out to study the expression profiles of the genes at different developmental stages. The results show that introns are absent in both SPITI paralogs. SNPs, Indels, and variable simple sequence repeats (SSR) were present in the SPITI1 paralog, however, only SNPs were identified in the SPITI2 paralog. The predicted SPITI1 protein had 168, 172, or 174 amino acid residues, and molecular weights ranging from 17.88 to 18.38 kDa. In contrast, SPITI2 coded for a protein with 192 amino acid residues, with molecular weight ranging from 20.59 to 20.65 kDa. All conserved domains of ITI proteins were present in both protein isoforms. Phylogenetic analysis indicated that SPITI genes were more closely related to I.trifida and I.triloba than I.nil, thus, suggesting their evolutionary relationship and conservation. A qPCR study indicated that both SPITI genes were expressed in all the sample tissues, though relative expression values differed across tissues at different developmental stages. This is the first study reporting diversity of SPITI genes and of an ~18 kDA isoform in sweetpotato. The findings may enable design of genetic engineering strategies for SPITI genes, including CRISPR/Cas gene editing in sweetpotato.

molecular biology↗

bioRxiv2022

A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. Hillquist)

BackgroundBlackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red raspberry (R. idaeus), and R. chingii, but very few genomic resources exist for blackberries and their relatives in subgenus Rubus. FindingsHere we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession Hillquist (R. argutus). Hillquist is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The Hillquist assembly, generated using PacBio long reads scaffolded with Hi-C sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on seven chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted using the assembly and Iso-Seq and RNA-seq data, of which 72% were functionally annotated. ConclusionsThe utility of the Hillquist genome has been demonstrated here by the development of the first genotyping-by-sequencing based linkage map of tetraploid blackberry and the identification of several possible candidate genes for primocane-fruiting within the previously mapped locus. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.

genomics↗

bioRxiv2021

Domestication Reshaped the Genetic Basis of Inbreeding Depression in a Maize Landrace Compared to its Wild Relative, Teosinte

Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to rare large-effect variation versus potentially more common variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load predicted from sequence data in the maize population. For many traits - and more commonly in maize - genetic variation among selffertilized families was less than expected based on additive and dominance variance estimated in outcrossed families, suggesting that a negative covariance between additive and homozygous dominance effects limits the variation available to selection under partial inbreeding. We identified quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, smalleffect recessive variation underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following to the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against large effect variants, but polygenic load is harder to purge and segregating mutational burden increased in maize compared to teosinte.

evolutionary biology↗

bioRxiv2020

Sequencing depth and genotype quality: Accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops

The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: i) do polyploid crop breeders need to invest more for additional sequencing depth? ii) how many markers are required to make selection decisions? iii) does considering non-additive genetic effects improve predictive ability (PA)? iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; [≤] 1000) are adequate for prediction, hence it is possible to get this number at the current sequencing depth from most service providers. We also show that considering dosage information and additive-effects only models had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations. Key messagePolypoid crop breeders do not need more investment for sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture.

genetics↗

bioRxiv2019

Unraveling the hexaploid sweetpotato inheritance using ultra-dense multilocus mapping

The hexaploid sweetpotato (Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and has a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly implemented software, MAPpoly. The resulting genetic map revealed 96.5% collinearity between I. batatas and its diploid relative I. trifida. We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%) were also observed. Except for low levels of preferential pairing in linkage group 2, we observed a hexasomic inheritance mechanism in all linkage groups. We propose that the hexasomic-bivalent inheritance promotes stability to the allelic transmission in sweetpotato.

genetics↗

bioRxiv2019

Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population

In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. (2n = 6x = 90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can only fit a single QTL and are generally hard to interpret. Here we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato bi-parental population ( Beauregard x Tanzania) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly predicted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every cM position. Multiple interval mapping was performed using our R package QTLPOLY and detected a total of 41 QTL, ranging from one to ten QTL per trait. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits and provided basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions allowed us to characterize additive allele effects as well as to compute QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.

genetics↗