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Building resilient food systems for Sub-Sahara Africa through genomics assisted breeding

And te tide and te time þat tu iboren (time and tide wait for no man)

In traditional African setting, we say time waits for no man and doesn’t spare the women either. At exactly half past five ante meridiem in East Africa, the cock crows, a woman (Kanini, meaning the little one) slowly stretches from her ricket-legged wooden bed covered by a thin mattress almost the inch of a tongue. She knows she is lucky, yet every morning when she opens her eyes to a so-called new day, she feels like closing them again. Half asleep, but the chores of the day must be attended to, the children, goats and her quarter acre farm, she pauses to think. Beside the bed are her three children sprawled across a mat on the floor covered with a piece of blanket, she glances across the room and looks at the four goats standing at the left corner of their one room grass thatched house, the only place they call home.

As a matter of priority, the goats must make room for the children to prepare and head to school. The goats are taken out and tied outside a tree standing tall at the entrance of the house, in front, is a heap of fresh red soil covering the grave of Kanini`s husband who was killed in a recent community conflict for pasture and water. He died a hero, she slowly shakes her head. Quickly the children are woken up and start their daily routine. Freshening up is categorical, smearing tiny faces with water droplets almost the volume of a single spit, their feet are left to be cleaned another day. As if it is an inherited trait, this habit seems to have been instilled in them since conception, careful, they must save the little water there is to spare their mother the agony of walking the whole day in search for water. They gulp a cup of porridge to the last drop knowing so well it probably may be the only meal of the day, and off they ran to school.

The goats stretch on their ropes and reach staggered grass growing behind the hut. They too know that they must feed before the sun is hot and the grass too course to chew. After milking, the goats are tethered to a shadier tree where they can browse. The fiery ball in the sky peeps out in the clouds as if in a rage, Kanini must head to weed her farm before the roasting sun is overhead. She stares at her farm and reminds herself that life is really generous to those who pursue their destiny and she must do so. The thin maize stocks and feeble bean stems are scattered across the farm with some already drying up. The sweetpotato hills, although looking weather beaten, are the only green healthy looking plants in this farm, an only hope for this household, people and goats. The sweetpotato leaves looks mottled, a sign of an unexpected visitors in the farm, viruses. Curious, Kanini digs another hill a few steps from where she is standing, bewildered, the young ones of the devastating sweetpotato weevils are struggling for breath under the hot soil. She is hopeful for a better tomorrow although the crops are almost withering she tends to them just in case luck is on the human side for drizzle of rain. As she leaves the farm she carries a few vines for the goats so that they can cheat their stomachs and survive till the next day.

The gods must be crazy” she sighs, not another failed season, the climate changed much, she even can’t predict what will happen next. Like the alchemist, she wishes she can understand the forces of nature. Kanini`s situation is not unique, it is the same script but a different cast all over Africa.  Overview of the state of food insecurity and malnutrition in Africa shows that more than one quarter of the population in Africa is suffering from hunger (FAO 2017). The report finds that more efforts are needed with regard to policies and programmes in order to achieve Sustainable Development Goal (SDG) Target 2.1 to end hunger by 2030. In addition, efforts to improve agricultural production must be accompanied by action to increase resilience.

SpeedBreeders and Genomics CoP visit Rubona Research Station in Rwanda

In sub -Sahara Africa, starchy crops such as sweetpotato can be used as the staple food, additional or as a food security crop. As a food security sweetpotato storage roots can be kept in the ground and harvested when needed to provide a continuous food supply during the off season with no requirement for expensive storage infrastructure. It becomes important in the diet seasonally, typically in the month or two before the major grain harvest or when the grain stock from the previous year has been exhausted. Sweet potato also provides a food reserve when the major grain crop fails because of drought and pest infestation. Storage roots can be boiled, baked or roasted with some people preferring to eat them raw. Sweetpotato leaves are also nutritious containing a good source of protein and vitamins A, C and B2 (riboflavin). Climate change is real, and that, we must embrace. Regions that used to receive adequate rainfall are now witnessing less, delayed rainfall or nothing at all. Communities often see a rise in hunger and further decline of local livelihoods in successive months, as farming families struggle with the knock-on effects of multiple droughts. Given the ailing nutritional status of many children and women plus the fact that many food sources which typically provide these nutrients are not as drought tolerant, the sweetpotato, with its high nutritional content, is a very important food source.

The genomic tools for sweetpotato improvement project (GT4SP) is an ambitious project to sequence sweetpotato and develop modern breeding tools for a food crop that sustains millions of people in SSA. This multi-partnership project lead by North Carolina State University is collaborating with; Boyce Thompson Institute at Cornell, Michigan State University, University of Queensland, Australia; The International Potato Center, Peru; Biosciences East and Central Africa, Kenya; National Crops Resources Research Institute, Uganda; Crops Research Institute, Ghana.

The differences that distinguish one plant from another are encoded in the plant’s genetic material, the DNA that comes from each parent is packaged in chromosome pairs (strands of genetic material). The genes control a plant’s characteristics and are located on specific segments of each chromosome. Together, all of a plant’s genes make up its genome. Some traits, like flower color, may be controlled by only one gene. However, other more complex characteristics like crop yield or starch content (which to high extent contributes to high dry matter in sweetpotato) may be influenced by many genes. Traditionally, plant breeders select plants based on their visible or measurable traits, called the phenotype. These breeding methodologies have extensively proven successful in development of plant cultivars and improvement of sweetpotato germplasm. Most renowned example is the orange fleshed sweetpotato (OFSP) that worn the World Food Prize 2016. Conventional breeding, however is still dependent to a considerable extent on subjective evaluation and empirical selection. The process can be difficult, slow, influenced by the environment, and costly – not only in the development itself, but also for the economy, as farmers suffer crop losses.

Molecular marker assisted breeding (MAS) also interchangeably used as marker assisted breeding (MAB) offers great challenges, opportunities and prospects for conventional scientific breeding, needs less subjectiveness and more science, i.e. practical and accurate evaluation, and effective and efficient selection. MAS can allow selection for all kinds of traits to be carried out at seedling stage and thus reduce the time required before the phenotype of an individual plant is known. For the traits that are expressed at later developmental stages, undesirable genotypes can be quickly eliminated by marker-assisted selection (MAS) by crossing selected individuals within or between themselves. MAB is not affected by environment, thus allowing the selection to be performed under any environmental conditions (e.g. greenhouse and off-season nurseries). This is very helpful for improvement of certain traits that are expressed only when favorable environmental conditions present, e.g. disease/pest resistance and stress tolerance. For low-heritability traits that are easily affected by environments, MAS based on reliable markers tightly linked to the quantitative trait loci (QTLs) for traits of interest can be more effective and efficient than phenotypic selection.

Using markers such as SSR and SNP, where both alleles of a gene pair are fully expressed (co-dominance), MAB can allow effective selection of minor (recessive) alleles of desired traits in the heterozygous status. No selfing or test crossing is needed to detect the traits controlled by recessive alleles, thus saving time and accelerating breeding progress. For the traits controlled by individual or multiple genes/quantitative trait loci (QTLs) in the same individuals can be identified and selected simultaneously in MAB, and thus MAB is particularly suitable for gene pyramiding. In traditional phenotypic selection, however, it is problematic to distinguish individual genes/loci because one gene may mask the effect of others. Genotypic assays based on molecular markers may be faster, cheaper and more accurate than conventional phenotypic assays, depending on the traits and conditions, and thus MAB may have higher effectiveness and efficiency in terms of time, resources and efforts saved. The genomic tools for sweetpotato improvement project has developed a genotyping by sequencing (GBS) protocol and a pipeline that will be used to handle the hexaploid sweetpotato high-throughput genotyping. The project is also addressing software alogarithms issues that fits this kind of genome.

Since not all markers are applicable across populations due to lack of marker polymorphism or reliable marker-trait association. Before the reward there must be labor-Ralp Ransom- GT4SP has developed several genetic mapping populations and collected high quality data for various traits of interest to be used in trait dissection and better help understand marker allelic diversity and genetic background effects. Such traits include resistance to sweetpotato virus disease (SPVD), weevil resistance, yield and yield components, drought tolerance and quality traits. We are in the process of evaluating other breeder-relevant multi-parent populations for more applied breeding projects. In addition, QTL positions and effects will need to be validated and re-estimated by breeders in their own germplasm of interest.

The application of molecular markers has the ability to enable breeders to select germplasm and breeding lines on the basis of a simple cost-effective DNA assay without the need to undertake extensive phenotypic evaluation. These markers must be reliable and closely linked to reduce the probability of recombination. The procedure must be straight forward so that it can be done in a timely manner within a breeding program and it must be efficient to enable significant cost and time savings. Extensive studies are being done by GT4SP on the use of a genomics selection model (GS), a new approach for improving quantitative traits in large plant breeding populations that uses whole genome molecular markers (high density markers and high-throughput genotyping). Genomic prediction also being referred to as “Breeding by Design” combines marker data with phenotypic and pedigree data (when available) in an attempt to increase the accuracy of the prediction of breeding and genotypic values. Implementation of GS in breeding programs should help speed up genetic gains and, as a result, improved, higher yielding, broadly adapted, and stable genotypes will be delivered at a much faster rate.

The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. The finalized sweetpotato reference genome assemblies of I. trifida and I. triloba (v3) together with the user friendly Jbrowse are making the MAS in sweetpotato a reality Identification of SNPs is very challenging in species with high levels of heterozygosity and/or with complex ploidy levels, as pseudo-SNPs are identified by misassembly of paralogs, sweetpotato is one of those crops. The aligment difficulties often associated with the use of short reads (like those produced by GBS) are less problematic in species for which available reference genomes facilitates SNPs calling and genome positioning of genetic variation. Availability of whole-genome and transcript sequences provides considerable data resources for SSR marker development. A good example is the use of the I. trifida and I. triloba genomes to mine markers from the genes along the beta carotene pathway or disease clusters and validating them in known phenotypes for MAS.

The breeders will need a granary for that will be the storehouse and management of the phenotypic and genotypic data, the Sweetpotato base has been constructed and continue to be improved to make sure data weevils and borers do not destroy the data that a lot of man-hours have been spent on it. The base is coming with breeder friendly analytical tools- Highly Interactive Data Analysis Platform (HIDAP) for data analysis and sweetpotato ontology for unified naming of traits to allow proper use of SPBase.

 “Genomic tools with no information on how to use is like machine without a manual”. GT4SP is not taking chances, the project has laid a strategy and developed a very good capacity building to empower the African sweetpotato breeders to be able to translate the research into applied breeding in their programs. Training workshops sessions combine both presentations and hands-on experiences. carefully designed, avoiding to rely only on the presentation-discussion style but rather an interactive workshop style, using exercises, case studies, field visits and other elements of experiential learning to build capacities. Taking advantage of the digital era, GT4SP is also training streaming live webinars from partners working on different aspects of the project to the African continent, for instance Michigan State university and North Carolina state University. In my village, we say if you have a rich neighbor, you too are rich, the Biosciences eastern and central Africa (BecA) has a capacity building program- the African Biosciences Challenge fund (ABCF). Through this program, we are doing long term training (6 months to 1 year) to African sweetpotato breeders on molecular research who will become the next generation breeders. Short term trainings at the BecA-ILRI hub are carried for a period of two weeks and this too we are making use of it. Capacity building is a long story whose words cannot fit here, in a nut shell, GT4SP is using a mixed model approach to train a cohort of breeders and scientist that will apply genomics assisted breeding.

To this day, sweetpotato breeding and improvement has come a long way. We conclude that the crop has great potential in the light of imminent challenges associated with its genetic complexity, emergence of new diseases and pests and climate change. With genomic tools, who knows it may become the number one crop in the world!

Our deep respect for the land and its harvest is the legacy of generations of farmers who put food on our tables, preserved our landscape, and inspired us with a powerful work ethic -James H. Douglas, Jr.

About Mercy Kitavi


  1. Great story, Mercy – bringing the relevance of MAS to the ground (and roots)!

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