Abstract
Elite parental lines are more likely to breed fine varieties, but knowledge about elite parents and their genetic backgrounds is limited. In this paper, we investigated the pedigree relationships of potato varieties bred worldwide and in China. Several elite parents were identified, and these parents were more frequently used as parents in breeding programs across different time periods and countries. We next used 2b-RAD, a reduced-representation sequencing method, to genotype the elite parent Mira and 24 of its offspring. These cultivars span 5 generations, making this lineage the longest continuous pedigree among Chinese bred potatoes. A total of 47,314 tetraploid single nucleotide polymorphisms (SNPs) identified by FreeBayes were used to trace the conserved segments of the Mira genome. The conserved segments had identical or similar allele-specific SNPs across the analyzed genotypes. In Mira, 3,788 segments comprising over 10,000 bp, or 20.8% of the genome, were defined as conserved segments. These segments contain genes involved in crucial biological processes that are of special interest to breeders. These regions, which have been conserved across generations of highly selective breeding, may be helpful for further breeding and performing genome-wide breeding by design.
Highlights
Potatoes (Solanum tuberosum L.) were first cultivated in China between 1573 and 1620 (Sun, 2003) and spread gradually to the entire country
An online potato pedigree database, developed by Wageningen University and consisting of over 8,000 genotypes bred in 68 countries, reflects most of the potato breeding history worldwide
After 2000, 330 cultivars and only 2 genotypes were listed as a direct parent >10 times (Table 3), and 57 genotypes were listed as the direct parent ≥3 times (Table 2 and Supplementary Table S2). These results indicate that some genotypes were used as parents more frequently in potato breeding and that more germplasm was used in potato breeding after 2000
Summary
Potatoes (Solanum tuberosum L.) were first cultivated in China between 1573 and 1620 (Sun, 2003) and spread gradually to the entire country. A large number of varieties were introduced from abroad and some of these evolved into farm varieties ( called indigenous) during this process. Some of these farm varieties are still grown in China (Sun, 2003). The modern potato breeding program in China began in the 1930s, starting with the introduction of varieties such as Katahdin, Epoka, Mira, Anemone, and Schwalbe as well as the varieties selected from imported lines such as Xiaoyezi and Duozibai, to launch crossbreeding programs around the country. Chinese potato breeding programs are cooperative with institutions around the world. Over 600 varieties have been bred, and the Chinese-bred variety Kexin 1 is planted on nearly 0.8 million ha every year (Duan, 2013)
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