Paul Gepts

Dept. of Plant Sciences

University of California, Davis

Journées 2017 Labex Agro

Agropolis Fondation

20 octobre, 2017

Domestication des plantes et biodiversitéC’est quoi?

Pour quoi l’étudier?

Application au theme de la journée: production agricole durable et transition agroécologique

La contribution des agriculteurs à la conservation de la biodiversitéPlusieurs examples de Mexique et de l’Ouganda

Conclusions

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(c) Paul Gepts 2017

Laidig et al. (2014) Genetic and non-geneticlong-term trends of 12 different crops in German official variety performance trials and on-farm yield trends. TAG

Cassman KG, Liska AJ (2007) Food and fuel for all: realistic or foolish? Biofuels, Bioproducts and Biorefining 1: 18-23

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Grain

maize

Forrage

maize

Oilseed

rape

Sugar

beet

(c) Paul Gepts 2017

Evolutionary process: selection for adaptation to human-induced environmental conditions, standing or de novo variation

Cultivation is a necessary condition, but the selective environment in an agroecosystem can be quite different from that in a natural ecosystem: e.g., Pathogens, herbivores Abiotic factors: light, water, soil nutrients Reduced competition

More efficient production system: biomass per unit of surface and time: e.g., Loss of seed dormancy, shattering More compact growth habit Change in reproductive system: outcrossing selfing vegetative

propagation

Human consumption or utilization: selection for novelties Development: e.g., Brassica spp. Color, size, shape, and texture Reduction in toxic compounds

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Gepts 2004, 2014, 2017; Meyer et al. 2012; Meyer and

Purugganan 2014; Larson et al. 2014

(c) Paul Gepts 2017

Gepts 2014 Current Opinion Plant Biology 5

Wild ancestral types Primitive varieties Landraces Improved varieties

(c) Paul Gepts 2017

Gepts 2014 Encycl. Agricultural Sciences

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(c) Paul Gepts 2017

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(c) Paul Gepts 2017

(c) Paul Gepts 2017

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Haricots & maïs

Sauvages, MEX

Haricots & maïs

domestiqués,

en sympatrie avec

haricot sauvage, MEX

Haricots &

maïs

Domestiqués,

MEX

Haricots à rames, RWA

Haricots nains, CA, USA

Dempewolf et al. 2008

(c) Paul Gepts 20179

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Gepts 2017 Handbook Agric Biodiversity, modified from Burke et al. 2007

(c) Paul Gepts 2017

Dérive génétique

Sélection

Étape majeure dans l’évolution humaine

Etudes génétiques, évolutionnaires, et du

development

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Domestication is the outcome of a selection process that leads to increased adaptation of plant and animals to cultivation or rearing and utilization by humans, as part of the transition from hunting-gathering to agriculture until current times (Gepts 2004)

Application à la conservation et l’utilisation de la

biodiversité

Dom

est

icati

on

Genetic Diversity

Landraces

Advanced Cvs.

Wild

(c) Paul Gepts 2017

Domestication

& Evolution under

Cultivation

HumansCultural development:

knowledge of plants, animals

technology

Population growth

Economic opportunities/constraints

Biocultural diversity

EnvironmentClimate change

Contrast between dry and

humid season, cold and warm

Contrast between wild and

domesticated env.

Diversity of niches

Plant or Animal Morphology

Behavior

Genetics

Physiology

Evolution

Gepts 2004, 2006

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(c) Paul Gepts 2017

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Diversité

bioculturelle

Mexique

Italie

Ouganda

Georgie

Bolivie

Colombie

(c) Paul Gepts 2017

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Exemple 1: Les

fermiers cultivant des

poivrons (Capsicum annuum), Etat

d’Aguascalientes,

México(photos: K. Kraft)(c) Paul Gepts 2017

Selon le type de poivron: Frais: Caloro, Jalapeño, Hungaro,

Serrano, Anaheim, Bell Sec: Pasilla, Guajillo, Ancho,

Mulato, Puya, Huacle

Poivrons frais: semences commerciales en F1 (22%)

Poivrons sec: semences récoltées par fermiers ou obtenues chez d’autres (78%)

Sélection des semences par fermiers: maintenir un idéotype, plutôt qu’une sélection directionnelle: maïs (Cleveland et al. 2000), haricots (Worthington et al. 2012)

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Caloro Jalapeño Serrano Anaheim

Pasilla Guajillo Ancho Mulato

Kraig Kraft

(c) Paul Gepts 2017

Selection mostly after harvest: Importance of LD and multi-locus associations with seed traits in a predominantly self-pollinated crop

a b

Payró de la Cruz et al. 2005

weedy

domesticated

EXAMPLE 2: ARE FARMERS AGENTS OF SELECTION

AND GENE FLOW? CENTRAL MEXICO: MICHOACÁN-GUANAJUATO

Photos: D. Zizumbo 16

Patricia Colunga, Daniel Zizumbo

(c) Paul Gepts 2017

FARMERS MAINTAIN WIDE RANGE OF DIVERSITY

INCLUDING IMPROVED CULTIVARS AND WILD BEANS

WITHIN FIELDS

Average

seed

weight

(g/100)

Wild 6

Weedy 20

Domesticated 39

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Environs of Yuriria, Guanajuato, Mexico

Zizumbo-Villarreal et al. 2005

+ Flor de

Mayo

type

cultivar:

(c) Paul Gepts

2017

DIFFERENT GENETIC STRUCTURE IN W & D

Wild: less diversity within populations, more among populations compared toDomesticated

Higher gene flow in Domesticated: Diversity within landraces: outcrosses

Seed exchange among farmers

H h GST Nm

Wild 0.24 0.13-0.18 0.40 0.78

Landraces 0.26 0.22-0.29 0.26 1.40

Breeding

lines

-- 0.03-0.06 -- --

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Zizumbo-Villarreal et al. 2005

(c) Paul Gepts 2017

Example 3: Determinacy in PhaseolusBeans

• Function of the gene(s)?

o Gene for earliness bush growth habit

o Gene for meristem fate

• What is the origin of the alleles for

determinacy? How many alleles?

• Do different alleles have different value in

breeding? Phenotype, correlations, transmission

node

Indeterminate Determinate

P. vulgaris

P. lunatus

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Tanaka & Fujita 1979

(c) Paul Gepts 2017

MULTIPLE ORIGINS OF DETERMINACY

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Frame shift

Deletion of

entire coding

region

Exon-intron splicing failure

Non-synonymous substitution

Retrotransposon insertion 4171-4174 bp

• Multiple geographic origins

of determinacy = repeated

selection of the determinate

phenotype by farmers

• Applications to conservation

and breeding: same

phenotype in different genetic

backgrounds?

Kwak M, Toro O, Debouck D, Gepts P (2012) Annals of Botany 110:1573-1580

(c) Paul Gepts 2017

EXAMPLE 4: INTRODUCTION OF MARKET-TYPE BEANS, OAXACA, MÉXICO

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Worthington M, Soleri D,

Aragón-Cuevas F, Gepts P.

Crop Sci 2012

Soleri D, Worthington M,

Aragón-Cuevas F, Smith

SE, Gepts P. Econ Bot 2013

(c) Paul Gepts 2017

Margaret Worthington,Daniela Soleri

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Santa María Jaltianguis, OaxacaLower altitude fields

(c) Paul Gepts 2017

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THREE MAIN TAXA

Phaseolus coccineus & P. dumosus

Phaseolus vulgaris race Mesoamerica

Phaseolus vulgaris race Jalisco

M. W

ort

hin

gto

n, D

. S

ole

ri, &

P. G

ep

ts, C

rop

Sci

2012

(c) Paul Gepts 2017

Farmers know the temperature adaptation of taxa and plant the three taxa accordingly: high, medium, and lower altitude

Farmers have very different opinions about varietal differences: “lumpers” vs. “splitters”

Farmers “creolize” introduced cultivars to match them to local domesticates by allowing unilateral cross-hybridization [Female Local x Male Introduced] but not the reverse

Ideotype selection instead of directional selection (See Cleveland, Soleri et al. 2000)

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(c) Paul Gepts 2017

EXAMPLE 4: SEED ADOPTION AMONG FARMERS

IN WESTERN UGANDA (HOIMA DISTRICT)

Figure 1. A heuristic model of the formal (red), local (blue) and intermediate (green)

seed exchange networks.

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Seed

Storage

Planting/multiplication

Genebanks

Community seed banks

Exchange with “nodal” farmers

Market

Neighboring farmer groups

Diversity fairs

Development organizationsNGOs

Participatory seed

dissemination

Micro, small and mediumenterprises (MSMEs)

National Seed Certification

Service (NSCS)

UNBP, NaCRRI

CIAT-PABRA

Privateseed

companies

Private sector wholesalers

Internationalmarkets

PVS

Certified seed

Quality declared seed (QDS)

Erin Wilkus

Integrated seed systems

Household type

Number of surveyed households

Number of seedcollection households

Breeding program-affiliated 72 41

Akumulikire Women Group

27 11

Kakindo Sustainable Group

20 13

Kyamaleera Handcraft Group

25 17

Breeding program-unaffiliated126 41

Total 198 82

Household surveys + Seed genotypingvia SNPs (m ~ 5,400)

(c) Paul Gepts 2017

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Farmer group membership

Unaffiliated Akumulikire Kakindo

Mar

ket

All

sou

rces

House

ho

ld

Kyamaleera

Breeding-program affiliation

Affiliated

Org

aniz

atio

n

“SE” DJNG

Andean M

M

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• Market-purchased seed • Consistently represented a significant

majority of seed in household seed stocks

• Organization-sourced seed • Supplied a larger proportion of

Mesoamerican seed than other seed sources

• Breeding program-affiliated households• More likely to adopt organization

sourced seed, especially Mesoamerican seed

• More likely to allocate Mesoamerican seeds to experimentation than breeding program–unaffiliated households

(c) Paul Gepts 2017

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Adoption practices varied across farmer groups

Adoption-related outcomes varied

across farmer groups

Akumulikire was least likely to adopt

Akumulikire had the least diverse seed stock

Kyamaleera was more likely to adopt Andean varieties

Kyamaleera household-saved seed stock did not contain evidence of “Seed Engufu”

Kakindo was more likely to adopt Mesoamerican varieties and maintain household-saved Andean varieties

Kakindo was the only farmer group with “Seed Engufu” in household-saved seed stock and had highest overall genetic diversity

(c) Paul Gepts 2017

29(c) Paul Gepts 2017

CONCLUSIONS

Findings

Knowledge of farmers Morphological & adaptation Maintain genetic diversity by

promoting gene flow (creolization) Dynamic system in response to

market demand

Repeated selection Spatially Probably also temporally

What type of selection? Stabilizing selection: Maintenance of

type Directional selection? Yield?

Role of Participatory Varietal Selection and farmer groups

Application to Conservation & Breeding

Local conservation See also e.g., Brush, Zimmerer,

etc.) is important and worth it

Keep farmers on the farm! Favor rural life and local

production

Participatory or distributed breeding How can farmers evolve from

ideotype maintenance to directional selection?

What is the role of farmers & scientists?

30(c) Paul Gepts 2017