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

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.

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.

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

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)

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)

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

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

LISTS OF WORLD ORPHAN CROPS

(Varshney et al. 2012) Nature Biotechnology

Strategies to overcomes

bottlenecks in orphan crops

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

Push-Pull Concept in Cassava

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.

CASE STUDY

Scheme for Marker Assisted Selection (MAS) for Cassava Improvement

MAS Scheme To Improve Cassava Germplasm

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

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)

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)

SCHEME FOR MARKER ASSISTED SELECTION OF DESIRABLE GENES

MARKER ASSISTED SELECTION

Bidinger et al. (2005)

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

Abiotic stress:

Terminal drought is a major problem causing more than

50% production losses.

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

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.

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

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.

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.

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.

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

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

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.