SATrends Issue 20 
July 2002


1. Gerrymandering the Gene Pool

Part 3: Molecular Mapping

Continuing from Part 2 of the subject (Marker Development) published in last month’s SATrends, we now bring you Part 3 of the four part series.


A genetic linkage map shows the relative locations of specific DNA markers along the chromosome, similar to road-signs on a highway. A potential marker on a genetic map can be any morphological or molecular characteristic that is easily detectable and which defines the individual. Markers can be either genes or DNA segments that have no known function but whose inheritance pattern can be followed.


DNA sequence differences are especially useful markers because they are easy to characterize. Examples of other types of markers include (1) restriction fragment length polymorphisms (RFLPs), which reflect sequence variations in DNA sites that can be cut by DNA restriction enzymes, and (2) microsatellites or Simple Sequence Repeats (SSR), which are short repeated sequences that vary in the number of repeated units, and therefore in length. Markers must be polymorphic to be useful in mapping; that is, alternative forms (alleles) must exist among individuals so that they are detectable among different members in the mapping population.


A mapping population is the group of individuals that will be evaluated for their "score" at a set of markers. This raw data is then analyzed by software, which constructs the genetic map by observing how frequently the alleles at any two markers are inherited together. The closer the markers are, the less likely it is that a recombination event (a crossover during meiosis) will separate the alleles; consequently, the more likely it is that they will be inherited together. Therefore, unlike other types of maps, the distance between points on a genetic map is not measured by physical units, but rather is a reflection of the recombination frequency between those two points.


Linkage map copy.jpg (10092 bytes)Genetic map units are measured in terms of centimorgans (cM, named after the geneticist Thomas Hunt Morgan). Two markers are said to be 1 cM apart if they are separated by recombination 1% of the time. The genetic distance in fact tells us very little about the physical distance, which is the actual amount of DNA separating the markers. This genetic to physical distance relationship varies between species, and varies between different areas within the genome of a single species. Left: Sorghum Linkage Groups A, B, C, E & J, with mapped markers listed on the left hand side, and the genetic distance between the markers, in cM, on the right hand side.


Genetic maps help us understand the structure, function, and evolution of the genome. Research shows that the genetic maps of many closely related species (e.g., the cereals) are quite similar with respect to the content and location of genes, and scientists are trying to determine how the genetic map of one species may be applied to others.


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2.Peanut Paternity Suit?

Cultivated groundnut (Arachis hypogaea L.) is descended from two genomes, referred to as the A and the B genome donors.  Evidence clearly shows that the A genome donor is Arachis duranensis, and there is no ambiguity about it.


The problem has long been the B genome donor. Different species from the B genome pool have been proposed.  According to Singh and Smartt (1998) A. batizocoi is the donor. Kochert et al, (1991) based on RFLP studies, suggested A. ipaensis as the donor.  According to Paik-Ro et al (1992) A. batizocoi is not closely related to A. hypogaea and hence cannot be the B genome donor.  Karyotype studies of Fernandez and Krapovickas (1994) support A. duranensis and A. ipaensis as the A and B genome donors of A. hypogaea.


Inter-relationships of twenty-five species of Arachis, of which thirteen were from section Arachis, were studied by Randomly Amplified Polymorphic DNA (RAPD)-cluster analysis. A large number of primers were used in the study.  All the primers produced polymorphic bands. It was interesting to note that most of the species from different sections grouped together as per the classification of Arachis. The B genome species formed two groups placed away from each other.  One group comprised of A. batizocoi, A. ipaensis and A. magna.  The other group comprised of A. hoehnei, A. benensis and A. valida.  The A. hoehnei group showed closer relationship to cultivated species A. hypogaea, whereas the A. batizicoi group showed a distant relationship.

ABARACHIS copy.jpg (10201 bytes)

ICRISAT scientists studied the crossability relationship. Cultivated groundnut was crossed with A. hoehnei, A. benensis, A. valida, A. magna, and A. ipaensis.


Things became clearer when A. hoehnei was crossed with A. hypogaea and produced bold seeds without the application of growth regulators, indicating the lack of barriers. A few mature seeds were obtained.  Most of the seeds were bold but immature, and were germinated in vitro to obtain plants. Fertility in the hybrids was promising and ranged from 14-21 %.  On the other hand, crosses with A. benensis, A. valida, A. magna and A. ipaensis set immature seeds which were less than 3.0 mm in size.  This meant that these hybrid embryos aborted early, and the embryo rescue technique was necessary to obtain hybrid plants. The picture on the right shows A. duranensis (left) and A. hoehnei (right), with A. hypogaea below.


Crossability data supports molecular studies in showing a closer relationship between cultivated groundnut and A. hoehnei, where major portions of their genetic makeup are similar. Thus, based on molecular analysis, ICRISAT scientists propose A. hoehnei as the B genome donor of cultivated groundnut.


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3.The Winds of Change in West Africa

SAT agriculture is constantly changing. Population growth, liberalization, globalization, new agricultural technology, new cropping patterns and many other factors, have all contributed to change, for better or for worse. What changes have occurred at household level, in terms of food security, income, and livelihood opportunities?

A recent study by ICRISAT in Burkina Faso compared the current situation with data collected 15 years ago by ICRISAT. The earlier study covered 150 households in 3 agro-ecological zones differing in soil type, rainfall and crops grown. The same households were resurveyed, to see what had changed in this period. The major findings are:

  • Remarkable changes in household structure and composition
  • No major changes in rainfall
  • Large increase in population density in some zones
  • More wealth (more livestock, draft animals, and carts), largely due to profits from cotton cultivation
  • Greater use of animal traction and water conservation technologies
  • Improvements in institutions and infrastructure, e.g., more women’s groups that improved credit access and community support
  • Fertilizer use has increased due to better availability of fertilizer and higher returns to fertilizer investment on horticulture and cotton.  However, fertilizer use is still at very low levels.  Use of inputs and new technology is highest in high-rainfall areas, and on cash crops.

Burkina copy.jpg (9955 bytes)One significant trend is income diversification. Agriculture in a drought-prone region is highly risky, so farmers look for ways to supplement farm income with wage labor, petty trade, remittances, etc. Diversification into non-farm activities was greatest in the drier northern part of the country, while diversification within agriculture was more important in the wetter southern areas.

However, some caveats. Major policy changes since 1985 -- economic liberalization, structural adjustment programs, currency devaluation -- make it harder to compare the two datasets. The increase in assets/income is a robust trend: most people in these villages are better off than they were 15 years ago. In contrast, other parameters (e.g., relative importance of different income sources) are highly variable across locations and years.

The findings have implications for ICRISAT’s research priorities in West Africa. For example, economists and social scientists may need to study development pathways in order to help improve the targeting of development efforts. Plant breeders will need to address the reasons why improved varieties have given little yield advantage over landraces. In view of the increasing importance of livestock in the farming system, they may also need to increase their emphasis on dual-purpose cultivars that provide grain as well as fodder.

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4. Insect Problems? Try a Little Wax and Hair

Shoot fly 3.jpg (9252 bytes)Sorghum shoot fly, Atherigona soccata, is a particularly nasty pest of sorghum in Asia, Africa, and the Mediterranean area. Females lay single cigar-shaped eggs on the undersides of leaves at the 1- to 7-leaf stage. The eggs hatch after only a day or two of incubation, and the larvae cut the growing point of the leaf, resulting in wilting and drying. These leaves, known as ‘deadhearts’, are easily plucked. When a deadheart is plucked, it releases an obnoxious odor. Right, deadheart, egg on leaf, with the culprit in the inset.

Damage occurs 1-4 weeks after seedling emergence. The damaged plants produce side tillers, which may also be attacked. The shoot fly’s entire life cycle is completed in 17-21 days. In India, shoot fly populations begin to increase in July, peak in August-September, and then decline. Infestations are especially high when sorghum planting is staggered due to erratic rainfall. Infestation is normally high in the postrainy-season crop, which is sown in September-October. Temperatures above 35oC and below 18oC reduce shoot fly survival, as does continuous rainfall.   

To identify sources of resistance to shoot fly, we screened over 30,000 sorghum germplasm accessions at ICRISAT-Patancheru. Nearly 45 accessions with moderate levels of resistance have so far been identified in our sorghum germplasm collection, and improved varieties have been developed. These lines have resistance comparable to original sources of resistance, and their yield potential is greater than that of the landraces.

Considerable progress has been made in understanding the mechanisms of resistance to shoot fly in cultivated and wild relatives of sorghum. Oviposition non-preference (a bit of entomology-speak that refers to the female's disdain for laying eggs on a particular genotype) is the primary mechanism of resistance.

Shoot fly 2.jpg (9958 bytes)Why? The answer can be summed up in one word: wax. The glossy leaf trait of resistant lines in sorghum is caused by a smooth amorphous wax layer, along with a few wax crystals. Cultivars with high transpiration rates are therefore preferred, since resistant lines have low leaf surface wetness. Left, compare resistant lines with CSH-1, a susceptible line. Shoot fly 1.jpg (9401 bytes)

Right, the top half shows the waxy amorphous surface of resistant line leaves, and the lower half shows the dense mesh of crystalline flakes in the susceptible line.

Shoot fly-resistant genotypes impede the survival of larvae, as well as the survival, longevity and fecundity of females. Another defensive technique among some genotypes is an inherent ability to produce side-tillers after the main shoot is killed. These side-tillers can produce a reasonable yield if the plant is not attacked further.

Shoot fly-resistant lines grow more rapidly and have greater seedling height and hardness, longer stems and internodes, and shorter peduncles than susceptible lines.  Most shoot fly-reisstant germplasm lines have hairy appendages called trichomes on the undersurface of leaves.  Trichomes are absent in susceptible lines.

So, once entomologists and breeders identify lines with leaves that sport waxy flesh and hairy underarms, what’s next?

Efforts are under way to transfer shoot fly resistance into high-yielding hybrid parents and varieties. Efforts are also under way to rear shoot flies on artificial diets to identify Bacillus thuringiensis toxins for developing transgenic sorghums with resistance, and identify molecular markers associated with resistance to this insect.

If all this comes to pass, an end to the shoot fly havoc in poor farmers’ sorghum fields may be in sight.

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Highlights of Previous Issues:

June 2002: Gerrymandering the Gene Pool • Tribal Treasure Troves • The Return of the Native • Poverty and the Perch

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.