Construction of a high-density reference linkage map of tea (<i>Camellia sinensis</i>)

Abstract

A few linkage maps of tea have been constructed using pseudo-testcross theory based on dominant marker systems. However, dominant markers are not suitable as landmark markers across a wide range of materials. Therefore, we developed co-dominant SSR markers from genomic DNA and ESTs and constructed a reference map using these co-dominant markers as landmarks. A population of 54 F1 clones derived from reciprocal crosses between ‘Sayamakaori’ and ‘Kana-Ck17’ was used for the linkage analysis. Maps of both parents were constructed from the F1 population that was taken for BC1 population. The order of most of the dominant markers in the parental maps was consistent. We constructed a core map by merging the linkage data for markers that detected polymorphisms in both parents. The core map contains 15 linkage groups, which corresponds to the basic chromosome number of tea. The total length of the core map is 1218 cM. Here, we present the reference map as a central core map sandwiched between the parental maps for each linkage group; the combined maps contain 441 SSRs, 7 CAPS, 2 STS and 674 RAPDs. This newly constructed linkage map can be used as a basic reference linkage map of tea.

Worldwide core collections of tea (Camellia sinensis) based on SSR markers

“…As SSR markers for genotyping, we selected 23 loci from the core map of C. sinensis (Taniguchi et al 2012) to cover the whole genome evenly (Supplementary Tables 2 and 3). Polymerase chain reaction (PCR) was performed in a 10-μL reaction mix including 20 ng of total DNA, 10× PCR Gold buffer (Life Technologies, Carlsbad, CA, USA), 0.8 μL of 8 mM dNTPs, 0.1 U of AmpliTaq Gold polymerase (Life Technologies), 0.8 μL of 25 mM MgCl 2 , and 1 μM of each forward and reverse primer.…”

“…Polymerase chain reaction (PCR) was performed in a 10-μL reaction mix including 20 ng of total DNA, 10× PCR Gold buffer (Life Technologies, Carlsbad, CA, USA), 0.8 μL of 8 mM dNTPs, 0.1 U of AmpliTaq Gold polymerase (Life Technologies), 0.8 μL of 25 mM MgCl 2 , and 1 μM of each forward and reverse primer. The primer sequences are listed in Taniguchi et al (2012). The PCR reactions were carried out in a GeneAmp 9700 thermal cycler (Life Technologies) according to the following "touchdown PCR" cycling program: 95°C for 5 min, 95°C for 1 min, 62°C for 30 s, and 72°C for 1 min; 13 cycles at annealing temperatures decreasing by 0.5°C per cycle; and 25 cycles of 95°C for 1 min, 55°C for 30 s, and 72°C for 1 min, and a final 72°C for 10 min.…”

Development and characterization of single nucleotide polymorphism markers in Camellia sinensis (Theaceae)

“…The high frequency of SNPs presents high potential for the development of associated genetic mapping studies. For example, Taniguchi et al (2012) reported 3 new reference genetic maps for tea using 1124 markers, including 441 SSRs. The average distances between markers was 1.93 cM [cultivar (cv) 'Sayamakaori'], 1.85 cM (cv 'Kana-Ck17'), and 4.35 cM (core map, constructed by merging the markers present in both parents), respectively.…”

Molecular Markers

“…Thus, the reference map as a central core map is sandwiched between the parental maps for each linkage group; the combined maps containing 441 SSR, 7 CAPS, 2 STS, and 674 RAPD markers were developed. This newly constructed linkage map can be used as a basic reference linkage map of tea (Taniguchi et al 2007(Taniguchi et al , 2012.…”