Table 1 Country of origin, main traits interesting for breeders and sequencing statistics of 14 rice cultivars selected for genome sequencing in this study. Reads were mapped on the sequences of Nipponbare Os-Nipponbare-Reference-IRGSP-1.0. Number of reads, % of unique and duplicated reads and resulted mean coverages are reported. Number of total SNPs and number of total SNPs after filtering according to prediction significance, type and number of alleles and absence of repetitive sequences
From: Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions
Accession | Origin | Characteristic | Number of reads (× 103) | % unique reads | % duplicated reads | Mean coverage | SNPs vcf | SNPs filtered |
|---|---|---|---|---|---|---|---|---|
Arroz da Terra | Portugal | Cold tolerance, earliness | 80,492 | 78.9 | 0.14 | 39.9 | 465,830 | 117,170 |
Bahia | Spain | Parental, grain quality | 78,446 | 78.2 | 0.20 | 38.3 | 341,451 | 84,321 |
Bomba | Spain | Landrace, grain quality | 80,038 | 77.0 | 0.12 | 38.7 | 771,460 | 200,619 |
Gigante Vercelli | Italy | Blast resistance | 69,031 | 78.1 | 0.09 | 33.8 | 592,763 | 111,351 |
Gleva | Spain | Grain type | 78,505 | 78.6 | 0.12 | 38.7 | 564,829 | 141,363 |
Italica Livorno | Italy | Earliness, cold tolerance | 72,919 | 79.7 | 0.20 | 36.3 | 404,125 | 91,806 |
Kalao | France | Blast resistance | 75,052 | 76.9 | 0.13 | 36.4 | 1,025,081 | 253,553 |
L202 | USA | Parental, grain type | 78,854 | 77.1 | 0.14 | 38.3 | 989,104 | 269,476 |
Loto | Italy | earliness | 71,612 | 78.2 | 0.19 | 35.1 | 527,474 | 106,014 |
LTH | China | Cold tolerance | 77,667 | 77.7 | 0.10 | 37.8 | 573,944 | 149,950 |
M202 | USA | Parental | 69,364 | 79.1 | 0.14 | 34.5 | 669,310 | 124,931 |
Pavlovski | Russia | Earliness, grain type | 66,962 | 80.1 | 0.16 | 33.6 | 396,196 | 69,894 |
Puntal | Spain | Grain quality | 69,581 | 77.6 | 0.17 | 34.0 | 928,794 | 182,272 |
Senia | Spain | Grain type | 81,376 | 79.7 | 0.16 | 40.6 | 358,900 | 100,783 |