This document discusses marker-assisted selection for improving orphan crops. It provides examples of MAS for cassava, pearl millet, and chickpea. For cassava, markers can be used to select for resistance to cassava mosaic virus and reduce cyanide levels. In pearl millet, markers linked to drought tolerance genes can be introgressed. For chickpea, markers linked to drought tolerance quantitative trait loci and fusarium wilt resistance genes allow selection of these traits. However, limitations include a lack of resources, marker polymorphism, and integration with conventional breeding in orphan crops.

1. MARKER-ASSISTED
SELECTION IN ORPHAN
CROPS
PRESENTED
BY
ASHWANI KUMAR
Reg. No. – J-13-D-180-A
Division of Plant Breeding and Genetics
Sher-E-Kashmir University of Agricultural Sciences &
Technology, Jammu

2. WHAT ARE ORPHAN CROPS
 Orphan, abandoned, new, underutilized, neglected,
lost, underused, local, minor, traditional, forgotten,
alternative, promising, underdeveloped: these and
other terms are often used as synonyms for Orphan
crops.
 Orphan crops are those crops which are typically
not traded internationally but which can play an
important role in regional food security.

3. Twenty-seven orphan crops within developing
countries occupy areas of between 0.5-38 million ha
(Naylor et al. 2004).
Three criteria to be considered underutilized or
orphan crops
1. Proven food or energy value.
2. Plant has been widely cultivated in the past,
or the plant is currently cultivated, in a limited
geographical area.
3. Currently cultivated less than other comparable
plants.

4. In INDIA, the network which work on
orphan crops i.e. AICRN on UC
Different centres which work on orphan
crops:
1) Main Centres – 13
2) Cooperating Centres – 5
3) Voluntary Centres – 5

5.  Orphan Crops
A. PSEUDO-CEREALS
Grain amaranth (Amaranthus spp.)
Buckwheat (Fagopyrum spp.)
Chenopodium (Chenopodium spp.)
Job’s tear (Coix lacryma-jobi)
B. FOOD LEGUMES/ PULSES
Rice bean (Vigna umbellata)
Winged bean (Psophocarpus tetragonolobus)
C. OILSEEDS
Perilla (Perilla frutescens)
Paradise tree (Simarouba glauca)
D. VEGETABLES
Kankoda (Momordica dioica)
Winged bean (Psophocarpus tetragonolobus)

6.  FODDER CROPS
Amaranth (Amaranthus spp.)
Salt bush (Atriplex spp.)
Fodder tree species
 ENERGY, HYDROCARBON AND INDUSTRIAL PLANTS
Jojoba (Simmondsia chinensis)
Guayule (Parthenium argentatum)
Jatropha (Jatropha curcas)
Tumba (Citrullus colocynthis)
Paradise Tree (Siimarouba glauca)
Perilla (Perilla frutescens)

7. Some varieties released/identified at regional
level in different Underutilized crops by
CVRC based on their performance at multi-
locations in various coordinated trials.
For example:
High grain yield varieties :
Grain Amaranth- SKNA 21, RMA-4, RMA-7
Rice bean- VRB-3

8. MAJOR BOTTLENECKS IN ORPHAN CROPS
Due to lack of genetic improvement, these crops
produce inferior yield in terms of both quality and
quantity.
 Poor grain yield
 Poor in nutrient content:
 Abiotic stresses
 Hazardous or toxic products
- Cassava

9. LISTS OF WORLD ORPHAN CROPS
(Varshney et al. 2012)Nature Biotechnology

10. Strategies to overcomes
bottlenecks in orphan crops

11. CASSAVA
 Cassava (manioc; Manihot
esculenta).
 Major source of carbohydrates
are tuberous roots and leaves.
 Its strives well in marginal soils
and drought prone climates.
Cassava (Manihot esculenta)
2n = 2x = 36, 760bp

13. Push-Pull Concept in Cassava

14. Major problems in cassava crop are:-
1. Cassava mosaic virus (CMV)
2. Low protein content
3. Roots contain poisonous compounds called
cyanogenic glycosides (CG) which liberate
cyanide.
4. Konzo is a paralytic disease associated with
consumption of insufficiently processed
cassava.

15. CASE STUDY

16. Scheme for Marker Assisted Selection (MAS) for Cassava Improvement

18. MAS Scheme To Improve Cassava Germplasm

20.  Pearl millet (Pennisetum glaucum
L.).
 The major disease is downy
mildew & yield loss up to an 80%
 Marker assisted selection in pearl
millet for drought tolerance.
PEARL MILLET
Pearl millet (Pennisetum glaucum)
2n=2x=22, 2,450bp

21. DROUGHT AFFECTED AREA IN THE WORLD
The major bajra growing countries are Senegal, Mali, Niger, Nigeria, Sudan and India.
1.3 Billions people are under drought-prone areas (India/Africa)

22. Molecular plant breeding methods to address these
long standing problems of pearl millets production
Solution
i) Assess genetics variation for disease resistance
& drought tolerant particularly in land races, elite
breeding lines & other potential donor
ii) Identify molecular marker linked to specific
component of disease resistance & drought
tolerance
iii) Use the marker directly in the breeding
programme to follow the introgression of
desirable region of the genome.
(Howarth and Yadav, 2002)

23. SCHEME FOR MARKER ASSISTED SELECTION OF DESIRABLE GENES

25. MARKER ASSISTED SELECTION
Bidinger et al. (2005)

26.  Chickpea (Cicer arietinum
L.)
 Diploid (2n=2×=16) crop
with genome size of 740 Mb.
 The seeds of chickpea are
rich in protein (24.6%),
carbohydrate (64.6%) and
vitamins.
CHICKPEA

27.  Abiotic stress:
Terminal drought is a major problem causing more than
50% production losses.

28.  Based on the evaluation- minicore collection for terminal
drought tolerance- prolific root systems- identified and RILs
mapping populations were developed at ICRISAT: (Annigeri
x ICC 4958, ICC 4958 x ICC 1882 and ICC 283 x ICC
8261)
 A MABC breeding approach has been successfully
deployed in chickpea for enhancing drought tolerant by
introgressing “QTL-hotspot” into elite cultivars.
TERMINAL DROUGHT IN CHICKPEA

29.  Out of seven SSR markers present in the “QTL-
hotspot” region (ICCM0249, NCPGR127, TAA170,
NCPGR21, TR11, GA24 and STMS11), four markers
(ICCM0249, TAA170, GA24 and STMS11) available at
ICRISAT.
 “QTL-hotspot” has been successfully introgressed into
the genetic background of the 3 elite varieties i.e. JG11,
KAK2 and Chefe.

30. (Thudi et al. 2014)(Functional Plant Biology)

31.  Biotic stresses:
 Fusarium wilt reduces yield up to 90%
 Ascochyta blight may cause total crop loss
 Leaf spot
 Black root
 Pod borer is the major insect pest of chickpea and it
feeds on leaves and developing seeds.

32. Two major independent loci H1 and H2 determine the
resistance to race-1 in chickpea. The dominant alleles at both
H1 and H2 loci result in susceptible early wilting and
recessive at any one (h1h1H2H2 or H1H1h2h2) produce
susceptible late wilting and recessive at both the loci
(h1h1h2h2) result in resistance.
The primer CS-27F/ CS-27R, termed ASAP linked to the
allele for susceptibility at H1 locus and RAPD marker A07C
linked to H2 locus of susceptibility for fusarium wilt were
reported.
Single marker is not sufficient to identify resistant and
susceptible genotypes as there are two independent loci
governing resistance.

33.  The CS27700 marker linked to H1 locus was absent in all other
genotypes except JG62 and Karikadle. Other marker A07C417
linked to H2 locus was present in all genotypes except WR 315
and GBS964.
 The markers CS27 and A07C were present in susceptible (early
wilting H1H1H2H2) genotypes i.e. JG62 and Karikadle.
 Absence of both the markers indicated resistant (h1h1h2h2)
genotypes i.e. WR315 and GBS964.
 Presence of any one marker in other genotypes (K850, Bheema,
Vijay, A1, BG256, KAK-2, JG-11, BGD103, ICCV-2, ICC4958
and ICCV506) indicates susceptible but late wilter. These
markers can be used in MAS to speed up conventional breeding.

34. LOW IMPACT OF MAS IN ORPHAN CROPS
Resources (equipment) not available
Markers may be cost-effective
Accuracy of QTL mapping studies
QTL effects may depend on genetic background
or be influenced by environmental conditions
Lack of marker polymorphism in breeding
material
Poor integration of molecular genetics and
conventional breeding

35. Most important staple crops for many developing
countries
Model crop species
 Enormous amount of research
 In molecular genetics and genomics which has
provided enormous potential for marker
development and MAS
Costs of MAS are prohibitive so available
funding will largely determine the extent to
which markers are used in breeding
FUTURE OF MAS IN ORPHAN CROPS

36. CONCLUSION
 Orphan or Understudied crops provide food for resource poor
farmers and consumers in developing countries.
 They grow under extreme environmental conditions, many of them
poorly suited to major crops of the world.
 Green Revolution did not benefit from the positive effects of this
agricultural revolution that boosted the productivity of food crops in
the world.
 The next Green Revolution needs to also include these locally
adapted crops that are mostly known as orphan or understudied
crops.
 Although these crops are largely unimproved, the implementation of
modern improvement techniques on these crops has many
advantages.