Concepts and Measures of Crop Genetic Diversity and its ... · Indices that combine richness &...
Transcript of Concepts and Measures of Crop Genetic Diversity and its ... · Indices that combine richness &...
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