Genetic diversity and population structure of rice varieties grown in the Mediterranean basin. Spanish population, a case of study Concha Domingo domingo_concar@gva.es March 8 th 2017 ITRC-2017, Griffith Instituto Valenciano de Investigaciones Agrarias (IVIA)
where is Spain? Valencia, 39 28 00 N Tropic of Cancer Griffith, 34 17 24 S Tropic of Capricorn Northern latitude Temperate climate Hot and long days in Summer Cold and short days in Winter Tropic of Cancer 23 26 14 N Tropic of Capricorn 23º 26' 14 S
Rice production in Valencia environmental protected areas: surrounding L Albufera lake rice production destiny: national market japonica cultivars medium grain with white core L Albufera Lake 2013 Yield (Tm) area (Ha) Long grain Medium grain Total Total VALENCIA 10.025 104.904 114.929 14.759 ESPAÑA 397.471 475.218 872.689 111.984
The Rice Department Moncada Sueca
The Rice Department, more than 100 years of breeding Gavina Sarcet Sivert Cormorán Senia Alena Marjal Tebre Baixet Júcar Clot Leda Albada Niva Ullal Sequial Dosel Bahía Niva Liso Colina Balilla x Sollana Insen x Tremesino 1913 Albufera Antara Fleixa 2017 Argila JSendra
Plant evolution through the breeding program at IVIA Benlloch Bahía JSendra Fleixa <1913 1957 2005 2014
What we know about the rice history in Spain Most probably, the first rice seeds arrived in Spain in time of the Roman empire Its cultivation began in the XIII th and XIV th centuries, in time of the Arabians Breeding started in the XX th century, using local cultivars and cultivars from Asia as donors. ie. Chinese Originario There was a connection with the Italian breeding program Rice consumers set their preference in medium grain with a white core Long grain started to be cultivated in the 70th
photoperiod and temperature variations Rice expansion originated a wide genetic diversity 40ºN 300 ac 100 ac Tropic of Cancer After 1492 1500s 1000 ac 1900s Tropic of Capricorn 40ºS
Rice expansion originated a wide genetic diversity
Some aspects of tropical rice for breeding in temperate climate no heading in Summer (15 h day : 9 h night) High sterility in indica-japonica hybrids 110 cm indica japonica indica
cultivars travelled across regions with similar climate 40ºN Tropic of Cancer Tropic of Capricorn 40ºS
Breeding in temperate regions Assessment of genetic diversity and population structure of rice varieties cultivated in temperate regions
Assessment of the genetic diversity in temperate climate A collection of 217 cultivars cultivated in different countries
Working flow Genome sequencing of a selection of cultivars Generation of a SNP panel for analysing genetic diversity Genotyping (custom Infinium SNP genotyping array (Illumina) 2.096 SNPs
Selection of 14 cultivars representative of the genotypic diversity accession origin characteristic Bomba Spain Landrace, grain quality Arroz da Terra Portugal Cold tolerance, earliness Bahia Spain Parental, grain quality Senia Spain Grain type Gleva Spain Grain type M202 USA Parental Italica Livorno Italy Earliness, cold tolerance Loto Italy earliness Gigante Vercelli Italy Blast resistance LTH China Cold tolerance Pavlovski Russia Earliness, grain type L202 USA Parental, grain type Puntal Spain Grain quality Kalao France Blast resistance
Estimated LD decay temperate jap collection 3KRGP temperate jap Max(LD)/2 chromosomal distance between SNP pairs (Kb) 0,228 368,1 0,227 173,9 Spanish 0,230 698,9
indica collection Allele frequencies in the different subpopulations japonica collection
intermediate Bomba Genetic relationship among the temperate rice collection Population structure K2 K3 K4 K5 Italian Spanish I Spanish II American/ Australian Asian Old Spanish Long grain Round and medium grain
Principal Component Analysis Long grain Asian
Genetic relationship among the temperate rice collection neighbour-joining (NJ) tree 1.713 SNPs Darwin 6.0
Genetic relationship among medium grain cultivars
Bomba group Tall and low yielding cultivars Round grain White core High amylose content Very good cooking quality for Spanish traditional dishes Already cultivated in 1850 Bombita Bombilla Bombón Bomba Albufera
Genetic relationship among medium grain cultivars K5 K1 K4 K6 K2 K3
Bomba Benlloch Bahía JSendra Fleixa <1913 Bomba group <1913 1957 2005 2014 Old Spanish Spanish I Spanish II Asian rice 1st entry Asian rice 2nd entry American rice
Remarks Asian cultivars were introduced at least twice in Spain. In the eldest cultivars grown before 1900, the Asian influence from similar latitude regions is evident, most probably China, Japan or Korea. Before 1900, two types of rice were cultivated: Medium- grain type cultivars, that were improved through breeding programs, Bomba group, that remained invariable because of its cooking qualities. The initial breeding program used Asian cultivars as donors. In the second half of the 20th century, American germoplasm was introduced as donor in Spanish cultivars; which entailed a reduction in their height.
The team and the collaborators Concha Domingo Álvaro García Manuel Talón Luis Marqués, Copsemar Ester Sales, U. Zaragoza Generalitat Valenciana Ministerio de Economía, Industría y Competitividad
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