In spite of the limited investment in orphan crops, access to new technologies such as bioinformatics and low-cost genotyping opens new doors to modernise their breeding effectively. Innovation in plant breeding is imperative to meet the world’s growing demand for staple food and feed crops, and orphan crops can play a significant role in increasing productivity and quality, especially in developing countries. The short breeding history of most orphan crops implies that genetic gain should be achievable through easy-to-implement approaches such as forward breeding for simple traits or introgression of elite alleles at key target trait loci. However, limited financial support and access to sufficient, relevant and reliable phenotypic data continue to pose major challenges in terms of resources and capabilities. Digitalisation of orphan-crop breeding programmes can help not only to improve data quality and management, but also to mitigate data scarcity by allowing data to be accumulated and analysed over time and across teams. Bioinformatics tools and access to technologies such as molecular markers, some of them provided as services via specific platforms, allow breeders to implement modern strategies to improve breeding efficiency. In orphan crops, more marker–trait associations relevant to breeding germplasm are generally needed, but implementing digitalization, marker-based quality control or simple trait screening and introgression will help modernising breeding. Finally, the development of local capacities—of both people and infrastructure—remains a necessity to ensure the sustainable adoption of modern breeding approaches.

Modernising breeding for orphan crops: tools, methodologies, and beyond

There are many ways to assess or define the stress resilience of crop production, but ultimately the resilience of systems (and communities), i.e., an ability to survive and prosper, is driven by profitability. Here we review challenges for those who seek to bring about beneficial change in practice or policy as we translate novel crop science research findings into impacts on the food supply chain. While advances in plant and crop science are relevant to this challenge, the context of application is crucial here and this will mean that many other considerations, discussed below, will potentially moderate the impact on crop growth and yield of what could be the introduction of very significant breakthroughs in genetic gain. This paper considers opportunities for plant scientists seeking to address the world’s growing food security challenge by exploiting new understanding of the basis of crop stress resilience. Ultimately the local challenge is to increase the resilience of cropping systems and rural communities.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/fes3.105

Stress resilience in crop plants: strategic thinking to address local food production problems

/pdf/plant-breeding-capacity-building-in-africa-25kdcjkq6o.pdf

Plant breeding capacity building in Africa

Sorghum (Sorghum bicolor) is a well-known
agronomic crop of global importance. The demand for sorghum as a food crop
makes it the fifth most important cereal in the world. The grain of sorghum is
utilized for food and feed, whereas the sorghum biomass may have many other
uses such as for fodder, bioenergy or even for construction. Globally, sorghum
is consumed as a food crop and used for home construction primarily in the
developing world. The grain and biomass
yield of sorghum is drastically reduced by the parasitic plant Striga hermonthica which is endemic to
Sub-Saharan Africa. To date, only one sorghum gene, LGS1, has been characterized as a genetic mechanism that reduces S. hermonthica parasitism by altering
the strigolactone composition of the host root exudates which results in a
reduction of the parasites ability to germinate. To establish more durable
resistance additional genetic variation needs to be identified that reduces the
S. hermonthica parasitism in sorghum,
but also reduces the parasitic weed seed bank by promoting suicidal
germination. To that end, the PP37 multi-parent advanced generation inter-cross
(MAGIC) population was developed, originally as a recurrent selection
population that was developed to recombine sorghum accessions with different
putative resistance mechanisms to S.
hermonthica. Whole genome sequences were developed for approximately 1,006
individuals of the PP37 MAGIC population. The population was phenotyped for S. hermonthica resistance during the
2016 and 2017 growing season in Northwestern Ethiopia. There was significant
spatial variation in the S. hermonthica natural
infestations that were partially attenuated for with artificial inoculation.
The data was used to conduct a genome-wide association study that detected
several subthreshold peaks, including the previously mapped LGS1. The highly quantitative nature of S. hermonthica resistance confounded
with the complex spatial variation in the parasite infestations across a given
location make it difficult to detect highly heritable variation across years
and environments. In
addition to S. hermonthica resistance,
the plant architecture of the PP37 MAGIC was also assessed at a location in
Northwestern Ethiopia that is free of the parasite, as it significantly reduces
plant height. To asses plant architecture the total plant height, the height of
the panicle base, flag leaf height, and pre-flag leaf height were collected
using a relatively high-throughput barcoded measurement system. Sorghum head
exertion and panicle length were derived from this data. The actual measures of
plant architecture and the derived traits were used to conduct a genome-wide
association study. The high heritability of this trait demonstrated the
statistical power of the PP37 mapping population. Highly significant peaks were
detected that resolved the dwarf3
locus and an uncharacterized qHT7.1 that had only been previously resolved
using a recombinant inbred line population. Furthermore, a novel significant
locus was associated with exertion on chromosome 1. The random mating that was
utilized to develop the PP37 MAGIC has broken the population structure that
when present can hinder our ability associate regions of the genome to a given
phenotype. As a result, novel candidate gene lists have been developed as an
outcome of this research that refined the potential genes that need to be
explored to validate qHT7.1 and the novel association on chromosome 1. 

This research
demonstrated the power of MAGIC populations in determining the genomic regions
that influence complex phenotypes, that facilitates future work in sorghum
genetic improvement through plant breeding. 
This research however also demonstrates a large international research
effort. The nuisances and lessons learned while conducting this international research
project are also discussed to help facilitate and guide similar research
projects in the future. The broader impacts of this research on the society at
large are also discussed, to highlight the unique potential broader impacts of
international research in the plant sciences. The broader impacts of this
research include germplasm development and extensive human capacity building in
plant breeding genetics for developing country students and aspiring
scientists. Overall this research attempts to serve as a model for highlighting
the interdisciplinary nature and complexity of conducting international plant
science research, while also making significant strides in improving our understanding
the genetic architecture of quantitative traits of agronomic importance in
sorghum.

A Genome-wide Association Study of the Quantitative Resistance to Striga hermonthica and Plant Architecture of Sorghum bicolor in Northwestern Ethiopia

Plant breeders must keep abreast of the rapid evolution of new technologies, and also implement information management strategies that efficaciously handle the ever growing amount of data required for efficient integrated breeding. Updated training for breeders is critical to build relevant human resource capacity, particularly in developing countries whose breeding programs suffer a lack of staff with diverse expertise. The CGIAR Generation Challenge Programme is leading such a capacity-building initiative. A survey was conducted among course nominees to establish a baseline of breeder level of education, knowledge and skills in analyzing data and their involvement in molecular breeding programs. The breeders were mainly from three regions: West and Central Africa, East and Southern Africa, and South and Southeast Asia, and also included a few participants from North Africa. Many of the breeders from all the regions held or were working towards a PhD. Gender balance was low, principally in West and Central Africa, where less than 15% of the breeders were women. Between 57% and 73% of the breeders surveyed in the different regions were involved in molecular breeding projects at regional or international level. The Use of multiple software tools by individual breeders for data analysis was low for breeders from all the regions, with most using 1 - 3 packages. A lack of high data-analysis capacity will be a problem in an era where integration of genomics and phenotypic data in breeding programs is essential to efficiently deliver improved cultivars.

/pdf/evaluating-human-resource-capacity-for-crop-breeding-in-5dbffwxqh2.pdf

Ndeye Ndack Diop

Papers

Evaluating Human Resource Capacity for Crop Breeding in National Programs in Africa and South and Southeast Asia