- EURISCO: The European search catalogue for plant genetic resources. 43 countries, 400 institutes, 1.8 million accessions, and a vital part of Genesys!
- Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley. Salinity allele found in wild barley.
- Geographical distribution of traits and diversity in the world collection of pearl millet [Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] landraces conserved at the ICRISAT genebank. Plant height in Burkina Faso ranges from 80 to 490cm.
- Hardy Kiwifruit Genetic Resources. They’re wild.
- Deciphering Genetic Diversity in the Origins of Pepper (Capsicum spp.) and Comparison with Worldwide Variability. Diversity is decreasing in Ecuador.
- Simple Sequence Repeat (SSR) markers show greater similarity among morphologically diverse Date palm (Phoenix dactylifera L.) cultivars grown in Pakistan. Morphologically diverse varieties show little genetic diversity.
- Assessing climate adaptation options and uncertainties for cereal systems in West Africa. About the only thing that’s going to work is increased temperature resilience during flowering.
Dissecting pearl millet diversity
Our friends at ICRISAT have been busy describing their pearl millet collection, and their latest offering is a thorough analysis of the geographic distribution of morphological traits. That follows, among other things, a general review of the collection, and an analysis of latitudinal patterns in morphological diversity.
That last paper showed that although pearl millet landraces reach basically similar latitudes in both the N and S hemispheres (about 34°), there is much more cultivation north of the equator than south, as one would perhaps expect from the relative distribution of landmasses, except perhaps for the 15°–20° range, from which there is more cultivation south of the equator than north. Mid-latitude regions (15°–20°) in both hemispheres have proved the most useful as sources of material for developing high-yielding cultivars (they are early-maturing, producing long and thick panicles with large seeds). So it seems that southern hemisphere germplasm has a greater chance of being useful in breeding, although most cultivation is in the north. Another example of interdependence.
The latest paper ((Upadhyaya, H., Reddy, K., Ahmed, M., Kumar, V., Gumma, M., & Ramachandran, S. (2016). Geographical distribution of traits and diversity in the world collection of pearl millet [Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] landraces conserved at the ICRISAT genebank Genetic Resources and Crop Evolution DOI: 10.1007/s10722-016-0442-8)) goes in a lot more detail for individual traits. It’s very difficult to summarize patterns in 8 quantitative traits (days to 50% flowering, plant height, total and productive tillers per plant, panicle exsertion, length and thickness and 1000 seed weight) and 8 qualitative traits (panicle shape and density, bristle length, seed shape and color, endosperm texture, green fodder yield potential and seed yield potential) from 15,969 accessions from 30 countries. So I’ll limit myself to one recommendation. If you want to see huge variation in pearl millet height, go to Burkina Faso.
The deep history of barley breeding
A recent paper reported on the discovery of a bit of the barley genome where an allele from the wild relative, when homozygous, confers a 30% yield advantage over a popular German variety under saline conditions. ((Saade, S., Maurer, A., Shahid, M., Oakey, H., Schmöckel, S., Negrão, S., Pillen, K., & Tester, M. (2016). Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley Scientific Reports, 6 DOI: 10.1038/srep32586)) That of course is very interesting in its own right, but I want here to delve a bit into the methods, rather than the results.
The main tool used by the researchers at the King Abdullah University of Science and Technology in Saudi Arabia was a “nested association mapping population” of barley called HEB-25. That stands for ‘Halle Exotic Barley 25’. The Halle bit refers to the site of the German plant breeding institute where the population was made. Following the trail of references from the KAST paper takes you to a 2015 paper which describes the history of HEB-25:
The population results from initial crosses between the spring barley elite cultivar Barke (Hordeum vulgare ssp. vulgare, Hv) and 25 highly divergent exotic barley accessions, contributing an ideal instrument to study biodiversity. The exotic donors comprise 24 wild barley accessions of H. vulgare ssp. spontaneum (Hsp), the progenitor of domesticated barley, and one Tibetian H. vulgare ssp. agriocrithon (Hag) accession. Barke was selected since it was also used as a parent of a barley high-resolution mapping population and as a genetic stock for mutation screening.
To generate HB-25, F1 plants between Barke and those 25 diverse barley samples were backcrossed to Barke and then selfed three times to make a total of 1,420 lines, each with a mainly Barke background, but different bits of genome from the 25 other samples. The researchers in Saudi Arabia then “simply” identified which bits of whose genome are associated with increased tolerance to salinity.
A lot of work. But we can take the story even further back. How were those 25 diverse barleys chosen? Again, following the trail of references takes you to a 1999 paper:
The exotic donors were selected from Badr et al. to represent a substantial part of the genetic diversity that is present across the Fertile Crescent, where barley domestication occurred.
Badr et al. (1999) was a very academic study of the origins of barley using molecular markers that would now be sneered at, but were all the rage back then:
The monophyletic nature of barley domestication is demonstrated based on allelic frequencies at 400 AFLP polymorphic loci studied in 317 wild and 57 cultivated lines.
So there you have it, 17 years from basic work on the geographic distribution and history of wild barley diversity to the identification of a particular, tiny bit of that diversity that confers a yield advantage to the crop under salinity stress. It would probably be a lot faster now, but you can see why using crop wild relatives in breeding is a bit of an acquired taste. And also that basic diversity research is needed for successful applied breeding.
Brainfood: Organic penalty, Rye gaps, Sustainable diet indicators, Wheat evolution
- Commercial Crop Yields Reveal Strengths and Weaknesses for Organic Agriculture in the United States. The headline will be that organic yield is 80% of conventional, but the results are far more nuanced than that suggests.
- Genetic Distinctiveness of Rye In situ Accessions from Portugal Unveils a New Hotspot of Unexplored Genetic Resources. More collecting needed.
- A Consensus Proposal for Nutritional Indicators to Assess the Sustainability of a Healthy Diet: The Mediterranean Diet as a Case Study. 13 indicators of sustainability described, from “Vegetable/animal protein consumption ratios” to “Diet-related morbidity/mortality statistics.”
- Reconciling the evolutionary origin of bread wheat (Triticum aestivum). One slightly changed ancestral subgenome, one much-changed ancestral subgenome, and one weird hybrid subgenome involving the previous two plus another. Basically, we were insanely lucky to get wheat.
Brainfood: Lentil diversity, Cacao diversity, Larch distribution, Tea diversity, Salmon breeding, Ethiopian sorghum, Brassica differentiation, Biodiversity info, Human footprint
- Genetic Diversity of Cultivated Lentil (Lens culinaris Medik.) and Its Relation to the World’s Agro-ecological Zones. 352 accessions, 54 countries, 3 agro-ecological groups (South Asia, Mediterranean, N temperate) in USDA collection.
- Association mapping of seed and disease resistance traits in Theobroma cacao L. 6 and 1 markers, respectively, based on 483 unique trees in the International Cocoa Genebank, Trinidad (ICGT).
- Historic translocations of European larch (Larix decidua Mill.) genetic resources across Europe – A review from the 17th until the mid-20th century. Humans have moved material to areas outside its native distribution, and have mixed up genetically distinct populations in some places.
- Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm (Camellia sinensis (L.) O. Kuntze) Based on nSSR Markers and cpDNA Sequences. African material groups according to where it was bred.
- First the seed, next the smolt? Will salmon farmers learn the right lessons from plant biotechnology? I bet not.
- Geographic patterns of phenotypic diversity in sorghum (Sorghum bicolor (L.) Moench) landraces from North Eastern Ethiopia. There aren’t any. Patterns, that is.
- Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Similar heading and tuberous morphotypes in the two species are due to parallel selection on genes that diverged after duplication event.
- Assessing the Cost of Global Biodiversity and Conservation Knowledge. Golly, it’s expensive!
- Sixteen years of change in the global terrestrial human footprint and implications for biodiversity conservation. Human footprint hasn’t increased by as much as might be feared, but still extends over 75% of world’s land surface. Let the mashing up with crop wild relatives hotspots begin!