SATrends Issue 19 

June 2002


1.Gerrymandering the Gene Pool - Part 2
2.Tribal Treasure Troves
3.The Return of the Native
4.Poverty and the Perch
5.Highlights of Previous Issues

1. Gerrymandering the Gene Pool

Part 2: Marker Development

Continuing from the introduction last month on marker assisted breeding, we now bring you the first step in the 3-step process, marker development.

In order for scientists to conduct marker-assisted breeding , they require molecular markers (regions of the DNA) that reveal variations between germplasm lines or accessions, to be used as signposts or  flags. In this article we take groundnut as an example. This challenging crop has presented a major problem since there is very little genetic variation to be found in it, indicating a severe genetic bottleneck, which took place during its evolution. Nevertheless, scientists have persevered.

Simple sequence repeats (SSRs), also known as microsatellites, are usually  highly polymorphic DNA markers. These are repeated di- tri or tetra- nucleotide sequences (eg. ATATATATATA, or CGCCGCCGCCGCC, representing Adenine, Thymine, Cytosine, and Guanine), and variation is generated as a result of slippage during the DNA replication process, thereby frequently increasing or decreasing the number of repeat units. We use theis variation revealed in these sections of DNA for molecular mapping or diversity assessments.

Previous studies by USDA, Georgia, generated just six polymorphic SSR markers when . 100 or more markers are needed for making a genetic map. At ICRISAT we felt that perhaps if  we followed a similar methodology, but on a much larger scale using robotics, we might be able to reveal substantially more variation.

An ICRISAT scientist traveled to the University of Georgia, USA, and constructed two 27 000 clone genomic libraries and, using robotics (left, picture of QBOT machine used), gridded them onto membranes. The membranes were then probed for SSR sequences using radioactivity so that SSR containing clones could be identified on an X-ray. Positive clones, containing repeat sequences were sequenced and SSR primers were designed from them.

Back at ICRISAT, we are screening primers for their ability to detect variation in groundnut. A total of 108 from the two libraries revealed polymorphism in groundnut. This represents 38% and 52% 56.3% of the primers that amplified. The most frequent repeat motif was (ATT)n repeat, representing 31% of repeat sequences. This repeat motif was also more polymorphic with an average number of variants of 4.95.8, compared with a mean of 3.8 from all primers. This method for identifying microsatellites has proved to be particularly cost-effective and efficient in groundnut. The relatively large number of polymorphic markers identified should provide a basis for investigating genetic diversity, molecular mapping, and marker-assisted breeding in cultivated groundnut.

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2. Tribal Treasure Troves

The northern "tribal" belt of Andhra Pradesh state in India is not known for agricultural development. But a recent study shows that traditional wisdom can sometimes be as effective as hot new science.

The 800,000 tribals in this region are subsistence farmers, who use shifting cultivation with almost no inputs. They survive because over generations, they have developed and perfected agricultural practices suited to such an environment. What are these methods? Are they applicable elsewhere? ICRISAT tried to find out through a project funded by UK’s Department for International Development.

One key aspect was biodiversity – the protection and maintenance of traditional germplasm. The study focused on pigeonpea, a major crop in this region. Local landraces are considered to be ancestral wealth, guarded with care. Responsibility for maintaining seed stocks rests with the women of the household. (Right, branches hung up for drying on roof, prior to storage).

Seeds are always "chemically" treated before storage. First sun-dried, then mixed with protectants such as wood ash, seeds of the marking nut (Semecarpus anacardium), red earth, or a moist mixture of red earth and rock salt, applied as a protective coating. They are carefully stored. For example, pods are kept in a woven bamboo basket which is hung above the cooking fire -- the heat and smoke keeps away pests. Several storage structures are used, all made from locally available material – earthen jars, bamboo baskets "lined" with cowdung, and even more exotic devices. For example:

Leaf baskets. Leaves of the Bauhinia tree are stitched together to form a pot-like structure known as Dooba. The Dooba (left) is normally used for one or two seasons; a properly made basket can last for 5 years. Surprisingly, it is just as effective as the airtight plastic containers used in modern genebanks!

Bottle gourds. Farmers collect large ripe bottle guards (locally called Doki, right) from the field. The gourd is first dried, then emptied of its contents, then washed, and sun-dried. Seeds are mixed with ash and poured into the gourd, and the opening sealed with cloth or leaves.

These methods may sound primitive, but they work. Without expensive chemicals, using locally available material, "uneducated" farmers have been able to protect their seed, and conserve landrace varieties for centuries. Modern science is only just beginning to appreciate the power of indigenous wisdom; but as more such studies are conducted, small-scale farmers everywhere will be able to benefit from a combination of old science and new.

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3. The Return of the Native

Perceptions concerning the situation in Afghanistan have been shaped largely by the media. With images of war, destruction and hostility towards outsiders on their minds, ICRISAT researchers Richard Jones and Kate Longley recently arrived in Kabul with a certain amount of trepidation. But apprehension turned to relief when they were met at the airport by their colleague Farid Waliyar, dressed in traditional Afghan dress.

Waliyar (with turban, and his brother) was not in disguise. He is an Afghan by birth, and as far as we know the only Afghan in the entire CGIAR system. Prevented from visiting his homeland for 27 long years by political difficulties, he was thrilled to once again assume the native speech and customs of the land where he grew up.

What were ICRISAT scientists doing in Kabul?

Following the events of September 11th, USAID funded ICARDA to lead the Future Harvest Consortium for the Rehabilitation of Agriculture in Afghanistan. ICARDA, which has recently established an office in Kabul, invited ICRISAT and the Overseas Development Institute (ODI) – Dr Longley represents both organizations – to a Code-of-Conduct Workshop to develop Guiding Principles for Seed Regulatory and Seed System Support Interventions for Afghanistan.

The workshop was opened by Engineer Mohammed Sharif, the First Deputy Minister of Afghanistan’s Ministry of Agriculture and Livestock, and attended by over 80 participants from various international agencies, including CIMMYT, CIP, IWMI, IFDC, and several NGOs. ICRISAT made a presentation entitled Lessons from disasters: the need for new approaches to seed interventions. The presentation was based on ICRISAT, CIAT and ODI experiences from Africa.

During the working group discussions with Afghan partners, Jones, Waliyar and Longley strongly promoted the need to move away from relief towards a demand-driven seed supply system. Indeed, this fundamental premise formed the basis of ICRISAT’s recommendations to the Ministry. Although somewhat controversial, the recommendation was warmly received by the Ministry, which reflects the stated policy of the interim government to move away from the Soviet model towards a more market-driven approach. The challenge now is to engage with partners and development investors to change words into deeds – a challenge that the ICRISAT team is determined to pursue.

(Right, the Lowgar Valley to the south-west of Kabul. The valley was badly affected during the Soviet occupation when many of the fruit orchards were bulldozed because they provided refuge for Mujahidin fighters who would ambush Soviet patrols. Since that time a lot of replanting has occurred and the valley is again productive.)

Afghanistan and its resilient people are truly unique and deserve our support!

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4. Poverty and the Perch

Over half of Kenya’s rural population lives in extreme poverty, and the numbers are increasing. Poverty alleviation programs haven’t always worked, partly because we lack information on livelihood options for the poor, and on the role of institutions in poverty alleviation. ICRISAT is working with the University of East Anglia, UK, to better understand these issues. As part of the study, economists examined a cluster of five villages near Lake Victoria. Three are fishing villages, two rely more on smallholder agriculture.

The fishing industry employs over 80% of the community either directly or indirectly. Fishing provides income, but agriculture is still the key. Most families must grow their own food – but few are able to grow enough. Once the harvest runs out, they must buy their food from the market, or depend on hand-outs. (Left, fish market near Lake Victoria).

The study examined livelihood patterns in different segments of the community. The rich are able to make substantial investments (eg, buying and then renting out fishing equipment) that yield fairly large, stable incomes. The middle class makes more modest investments that give smaller and more variable returns. For example, some own shops where the daily take – revenue, not profit – is barely KSh 100 ($ 1.2). The poor are mostly laborers, working long, risky hours for low pay.

‘If you haven’t made your money already,’ said one villager, ‘then you never will.’ Poverty has increased and livelihood options have become more difficult. Fish catches are significantly smaller than they were 10 years ago, and fishermen are forced to spend more time on the water. The costs of equipment have risen sharply.

Farmers are equally hard hit. They do not grow cash crops because there are no markets. Yields of food crops are falling, due to drought, insect pests, and infestation by Striga weeds. The number of cattle has fallen by 75 percent since the early 80s, partly because cash-starved owners are forced to sell their animals to buy food or pay school fees for their children.

What livelihood options do these villagers have, and how do they make livelihood choices? What are the results – in terms of income, risk, nutrition, and sustainability? What institutions support or hamper their efforts? These studies are providing some of the answers. And as the issues become clearer, researchers and development investors can work together to help poor communities in Africa climb out of poverty.

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Highlights of Previous Issues:

May 2002: Gerrymandering the Gene Pool• Snap, Crackle, and Pop• Checking Africa's Pulse• High Tech for an Old Problem

April 2002: Disaster Relief with a Difference• From Crop to Tabletop• Golden Millet, Naturally!• The "Green" to "Blue" Water Continuum

March 2002: On the Wild Side• A Handful of Seed• Here's to Fungus - hic!

February 2002: 36 Percent -- and Rising• Of Stalk and Livestock• Stalking the Enemy• Sorghum Scoop from Mali

January 2002: Back to the Drawing Board• Weed Better, Weed Faster• With Minds of their Own!• Closing Ranks against the Pod Borer

December 2001: It's a bird! It's a plane! No, it's a Super scientist!•  Viva Sorgo!• Small is Big!• Abortion Leads to Rebirth

November 2001: Sorghum Products: Poised to Take Off• Cash from Cattle Food• Empowerment Through Technology• Outwitting an Unfair Bug

October 2001: Backing a Winner• More than a Thousand Words• Sowing a New Future for Eritrea• A Casting Coup: Farmers' Day 2001

September 2001: Don’t Get Left on the Shelf• Nigeria Targets ‘Groundnut Leprosy’• Two Heads Are Better than One• Desperately Seeking Seeds

August 2001: Finding Chinks in the Armour•Brazilian Farmers get a Boost from the Sahel• Sahelian Partners Smash the Ivory Tower • What You See is What You Get - Simulation Modeling for Successful Farming

July 2001: Balaji Makes IT Waves• A Hot Date in the Sahel • It All Adds Up • More from Less• That's the Way the Cookie Crumbles

June 2001: Space-Age Partnership in West Africa• Bad Taste is Good•• Out of Africa•• Seed Priming: Rhapsody in Simplicity

May 2001: Dodging Drought in Kenya• Vietnam and ICRISAT Save Watersheds• Farmers Enrich Malawi's Soils• Groundnut Mystery Disease Identified

April 2001: Women Farmers Guide Scientists in Namibia •  Ashta Puts it Faith in IPM • Sahelian Farmers Place Their Bets • China and Pigeonpea: Love at Second Sight

March 2001: Agriculture: an Ally Against Global Warming?• Breaking the Spell of Witchweed• Groundnut Taking Root in Central Asia and the Caucasus• Zimbabwean Smallholders Drive the Research Agenda

February 2001: Somalia: Seeds Deliver Hope Amidst Chaos• The CGIAR Fights Desertification in Africa• Creating the World's First Molecular Marker Map of Chickpea• Aflatoxin and Cancer: Cracking a Hard Nut in Developing Countries

January 2001: Things Grow Better with Coke®: Micro-fertilizer System Sparks 50-100 Percent Millet Yield Increases in the Sahel• Groundnut (Peanut) Production Accelerates in Vietnam •  Pigeonpea Broadens Farmer's Options in Sudan •  Private Sector Invests in Public Plant Breeding Research at ICRISAT.

December 2000: International Symposium on SAT Futures • Centers Team Up to Help East Timor • Spatial Variability in Watersheds • World's First Cytoplasmic Male-Sterile Hybrid Pigeonpea • Groundnut (Peanut) Variety Boosts Malawian Agriculture • National Researchers Persevere in El Salvador • ICRISAT Celebrates India-ICRISAT Day • ICRISAT and World Vision International Work Together in Southern Africa.