Concepts and Measures of Crop Genetic Diversity and

its Evolution and Management on Farm

Toby Hodgkin and Tony Brown

Coordinator, PAR and HRF Bioversity International,

Rome, Italy

Centre for Plant Biodiversity

Research

•The different

faces of diversity

What is diversity?

Agro

biodiversityprovides

ensures

ecosystem

services

supports

SDGs

Complementarity

Portfolio

Future options

Adaptability

Resilience

Production

Regulation

Support

Cultural values

1. No poverty

2. No hunger

3. Good health

5. Gender equality

6. Clean water

8. Economic growth

12. Responsible consumption

13. Climate change management

14. Life on water

15. Life on land

•BACC Project

Measuring genetic diversity – characters

What genetic characters are to be compared?

– genetic loci – averages over loci

– multiple loci – haplotypes

– DNA fingerprints

– morphological characters

– whole genotypes – clones

– populations or varieties

Sorghum landraces – A. Teshome

Genetic units for in situ research

• Many ways to score intraspecific diversity

• Variables can be difficult to standardise across countries and crops to enable comparability

• Farmer-named, or - managed varieties (landrace) as focal unit of selection and evolution

• Information on the names, the uses of each variety, and the characters farmers use to distinguish them.

• Coevolution of farmers’ names or their selection AND genetic makeup

The context: Structured Populations

• Hierarchy : Crop Species, Varieties, Populations / Fields

• Population Structure

• Population size and number

• Longevity and perenniality

• Networks, connectedness, nestedness (migration and gene flow)

• Metapopulations, subpopulation extinction and re-colonization

Diversity data – sources and decisions

• The crop species (which and why)

• Farms and communities (2 levels of sampling)

• Total crop area (farm and community)

• Number of traditional and modern varieties

(proportion of area devoted to traditional varieties)

• Number of farms to be sampled (and sampling

strategy)

• Area of crop (farm and community)

• Area of each variety (farm and community)

General ideas of diversity

Intuitively, diversity is a comparative concept – we

might compare

– pairs of gametes or individuals –

• whether dissimilar “evenness”, “lack of dominance”

• how dissimilar - (phylo)genetic distance “distinctiveness”

– Samples or groups of individuals –

• number of types “richness”

• variation in frequency of types “evenness”

– adjacent sites and gradients, spatial & temporal

changes

“beta diversity” and “divergence”

Three key notions of diversity

• Richness, is the number of different types present in the sample, or in the target population

• Evenness is the similarity in frequency of types (the lack of dominance of one type)

• Divergence is the difference between different samples or populations for the types that are present, or their frequency

The concepts of richness and evenness

•Richness = 9 (local varieties): A=B

•Evenness (less dominance): A>B

•Farm A •Farm B

•Are

a p

lan

ted

•Different varieties (v)

•V1

•V2

•V3

•V4

Richness & Evenness

Evenness diversity is high when the types in the sample have very similar frequencies.

When pi = the frequency of ith allele or genotype, and var (pi) = variance in frequency

of alternative types. One measure of evenness is

CV (pi) = coefficient of variation of allele or genotype frequencies

= {var ( pi ) }1/2 / mean pi

Percent of fields

Landrace identity number0.001.002.003.004.005.006.007.008.009.00

1 8 15 22 29 36 43 50 57 64 71

Landrace Overall Frequencies - 1993

EvennessRichness

Sorghum landraces in

Ethiopia, Teshome

(1996)

Indices that combine richness & evenness

1) Simpson Index of diversity (h),

Where v1 is the area under variety 1 grown by that farmer, v2 that under variety

2 and V = iNvi is the total area under the crop for the household.

• simple meaning – the probability of pair-wise dissimilarity

• as a probability, h can never exceed 1.0

• approaches a limiting value with increasing sample size

• depends on the frequency of the most common types

Indices that combine richness & evenness

2) I = Shannon -Weaver Information Index

I = - ipi loge (pi) I = 1, … k

• not bounded by 1.0

• “additive” across loci, or character combinations

• less dependent (than Simpson) on the frequency of most frequent

type

• less conceivable than is the Nei index (h)

• much less dependent on sample size than is Richness (k)

Population Divergence

• Divergence (D) between populations - the excess of the total

diversity (hT) over the average of the within-population

diversities (hT - average hW), expressed as a proportion of the total

diversity (hT).

D = (hT - hW) / (hT)

• This index of population or variety Divergence is based on Wright’s

F-statistics, and related to the estimates of Nei’s Diversity indices.

• Parallel alternative measures of Divergence can be based on the

Shannon-Weaver Information statistics.

•

Sorghum varieties in Burkhina Faso (100’s square m)

FARM BEL GAM KAR ZUL ZUG BUR Total Number Even

Bouda 50 25 100 175 3 0.57

Mare 25 25 50 2 0.50

Oued, Marc 50 50 1 0

Oued, Hami 50 25 100 175 3 0.57

Sampelga 25 25 50 3 0.50

Oued, Inou 50 25 75 2 0.44

Daki, Bouk 100 25 50 175 3 0.57

Daki, Bint 25 25 50 2 0.50

Total 300 75 75 50 275 25 800 6

AREAS of sorghum varieties (100’s square m)

Mean HH Richness 2.25

Variety BEL GAM KAR ZUL ZUG BUR Total

Total (8 farms) 300 75 75 50 275 25 800

WeightedFrequencies 0.38 0.09 0.09 0.06 0.34 0.03 1.000

WeightedAverage hT = .72 hW = .510 D = 0.29

•maize, beans,

chili, squash

•maize, chili, casava,

cotton, peanuts

•maize,

beans,

•sorghum,

cowpea, millet,

okra

•durum wheat,

faba bean,

barley

•sorghum,

durum wheat•rice, taro

•rice, barley, finger

millet, taro, sponge

gourd, pigeon pea

•Morocco •Hungary

•Peru•Ethiopia

•Mexico

•Vietnam•Burkina Faso

•Nepal

•Involved 60 national and local research and education institutes,

extension services and non-government organizations (PNAS 2008:

vol. 105, no. 14)

•Simple globally applicable diversity measures:

•Richness, evenness, and divergence• evenness, • and divergence

Landrace diversity on farm –

Global averages PNAS 2008 study

•Total number of households sampled = 2,041

•Total area in the project = 421,000 ha

•Percentage of farm area growing traditional varieties = 93%

•Household area for any one crop = 0.68 ha

•Farm richness of named traditional varieties = 1.82

•Farm evenness = 0.26

•Community richness = 14

•Community evenness = 0.70

•Divergence among farms within communities = 0.64

Nepal dataFinger Millet Rice Crop

Bara Kaski Jumla Bara Kaski Jumla Aver-

Total area of crop in community (ha) 0.7 133 35 618 303 81 6245

Number of modern varieties 0 0 0 20 6 0 4 (1.1)

Proportion of farm growing landraces 100 100 100 29 76 100 93

Number of farms sampled 18 146 173 89 162 180 67

Area of crop per farm (sqm) 400 2000 500 11000 4800 1200 8225

Farm (or HH) landrace richness 1.06 1.72 1.36 3.82 4.51 1.09 1.9

Average farm evenness (Simpson) 0.03 0.26 0.17 0.56 0.62 0.03 0.28

Community richness 6 24 12 33 63 21 12

Community evenness 0.75 0.68 0.59 0.89 0.93 0.60 0.69

Divergence-between /total (%) 96 62 71 37 33 95 62

• -LN(1-Farm evenness)

•0.0 •0.5 •1.0 •1.5 •2.0

•LN

Fa

rm ric

hn

ess

•0.0

•0.5

•1.0

•1.5

•2.0

•Black circle = staples

•Gray circle = pulses,

vegetables, etc

Landrace richness and evenness at the farm level

Above the line:

High dominance with richness

from varieties held at low

frequencies: Diversity is an

insurance to meet future need

Below the line

More even frequency distribution:

Farmers select varieties for

current needs

Landrace richness and evenness

at the community level

• - LN[1-Community evenness]

•0 •1 •2 •3 •4 •5

•LN

Com

munity

richness

•0

•1

•2

•3

•4

•5

•Pearson r = 0.81,

•Spearman r=0.73

•P< 0.001

•Open circle = outbred

•Semi filled = partial

•Gray circle = selfing

•Black circle = clonal

Relationship between farm area and divergence

LN Farm Area (>50sqm) (=X)

4 6 8 10

- L

N [1

-div

erg

en

ce

] (=

Y)

0

1

2

3

4

5

Y = 3.87 - 3.22 * X

White = outcrossing;

Semi-filled = partial

outcrossing;

Grey = inbreeding

Black = clonal.

Graph excludes farms with

< 50sqm per household

(i.e., home-gardens).

Communities with a larger number

of smaller farms diverge in varietal

strategies. This trend would help to

keep crop genetic diversity on-farm

Use No.

crops

N Farm

Richness

Farm

Evennes

s

Communit

y Richness

Communit

y evenness

Divergence

Major

Staple7 29 2.1 0.29 20.5 0.73 0.62

Others 8 42 1.65 0.23 9.5 0.67 0.65

Mann-

Whitney

test

NS NS * * NS

Major staples had the higher richness and

evenness at the community level

Overall trends for categories of crops,

classified by their use (PNAS 2008)

•Community and household area statistics and estimates of

diversity for traditional varieties in crops

Crop

Total

Area

(ha)

%

TV

area

Number

of HH

Ave

area

(ha)

Range community means

of household areas

(ha)

Average

Farm

Richness

(TV)

Average

Farm

Evenness

(TV)

Community

Richness (TV)

Community

Evenness (TV)

Average

Divergence

(TV)

Rice 22182 38%777

0.20

5neverknew0.035-

0.352.18 0.25 34.83 0.77 0.64

Barley 10790 98% 583 0.79 0.12-1.86 1.39 0.16 6.33 0.60 0.72

Maize 8588 97% 449 1.83 0.72-3.68 1.57 0.18 8.50 0.60 0.73

Cassava 4183 100% 159 0.48 0.26-0.63 2.05 0.33 60.33 0.96 0.66

Faba Bean 3825 100% 87 1.29 0.76-1.76 1.77 0.28 6.50 0.68 0.60

Durum Wheat 3064 82%87

0.340.35-1.67 1.49 0.21 3.50 0.57 0.64

Beans 2642 98% 524 0.98 0.0015-3.79 1.80 0.27 8.92 0.63 0.57

Pearl Millet 2365 100% 49 0.76 0.56-0.99 2.42 0.47 12.67 0.86 0.46

Peanut 2176 100% 96 0.51 0.22-1.09 1.69 0.24 7.50 0.70 0.63

Sorghum 1811 100% 52 1.25 0.95-1.72 4.25 0.69 23.33 0.91 0.25

Squash 1417 100% 562 1.65 0.0004-3.05 1.51 0.22 8.01 0.66 0.65

Okra 265 100% 51 0.36 0.309-0.397 2.22 0.48 10.00 0.80 0.40

Finger Millet 248 100% 337 0.09 0.036-0.20 1.38 0.15 14.00 0.67 0.76

Chili 30 100% 175 0.10 0.0001-0.19 1.42 0.16 6.17 0.70 0.76

Taro 24 100% 361 0.03 0.0069-0.053 1.44 0.12 17.20 0.65 0.81

Total

63,600High

Total

4074

High variation1.82 0.26 14 0.70 0.64

•High farm evenness: farm diversity

is not made up of one dominant and

other rare varieties

•Any two samples drawn at

random within a farm differed in

26% (within a community 70%)

of the cases

•High divergence: high potential

of any two randomly chosen

households within the same

community to grow different

varieties

•High richness: households and communities

harbored a large number of varieties

Crop species Major staple, source of

livelihood

Farm (household) and Community as two levels of

samplingFarmer decisions and

social network

Total area for this crop in the community (the entire

community, not just the sampled farms) Sample base, scaling up

and area effects

Number of modern or exotic varieties Genetic erosion

Proportion of the farm devoted to growing traditional

varieties (landraces) Overall context

Number of farms sampled in the community Survey reliability

Area of crop per farm averaged over farms that were

actually sampled Cross comparisons of

species and sites

Main purpose of each variable

Crop species Species specific data

Farm (household) and Community as two levels of sampling Multilayered

Total area for this crop in the community Units of area

Number of modern varieties What to count

Proportion of the farm devoted to growing traditional

varieties Actual vs Available

Number of farms sampled in the community Project bias

Area of crop per farm averaged over farms that were actually

sampled Consistency

Main problems with each variable