目的 通過全基因組數(shù)據(jù)開發(fā)梔子Gardenia jasminoides全基因組SSR分子標(biāo)記。方法 基于梔子全基因組序列，利用MISA軟件搜索SSR位點，從染色體長度、SSR數(shù)量、不同重復(fù)類型、不同重復(fù)頻次以及不同核苷酸類型的特征進行了分析。結(jié)果 梔子基因組共鑒定到117 037個SSR，長度在12～817 bp，平均長度為24.68 bp。梔子基因組全長為534.90 Mb，最長的為Chr09，長達110.58 Mb；最短的為Chr10，僅有30.74 Mb；SSR出現(xiàn)頻率為444.23 bp/個。完全型核苷酸共計102 001個，以二核苷酸數(shù)量最多，六核苷酸最少，其中長度大于15 bp的SSR共有64 283個，占比為67.61%；混合型核苷酸14 464個，占比12.36%。各染色體組上SSR位點的頻數(shù)密度在157～280個Mb，且SSR位點數(shù)量和染色體組長度呈高度相關(guān)。SSR在梔子的11組染色體中以Chr09最多為31 012個，Chr10最少為5 360個。不同SSR類型重復(fù)頻次范圍在4～81，重復(fù)頻次主要集中在4～20，占比高達96.30%。完全型核苷酸不同重復(fù)類型種類和不同重復(fù)基序類型分別有2 429、1 112種，其優(yōu)勢重復(fù)單元依次為T、AT、AAT、AAAT、AAAAG、AAAAAT，梔子SSR序列在一定程度上偏好于A、T所構(gòu)成的堿基。結(jié)論 豐富了梔子的SSR分子標(biāo)記數(shù)據(jù)庫，可為后續(xù)梔子的核心種質(zhì)構(gòu)建、遺傳多樣性分析、品種鑒定及分子標(biāo)記輔助育種等研究奠定基礎(chǔ)。

Objective To develop genome-wide SSR molecular markers for Gardenia jasminoides through genome data. Methods Based on the whole genome sequence of G. jasminoides, searching for SSR locis by using MISA software, and analysing the characteristics in terms of chromosome length, number of SSRs, different repetition types, different repetition frequencies and different nucleotide types. Results A total of 117 037 SSRs were identified in G. jasminoides genome, the SSRs length was between 12—817 bp, the average length was 24.68 bp. The full length of G. jasminoides genome was 534.9 Mb, the longest one was Chr09, which was 110.58 Mb, the shortest one was Chr10, only 30.74 Mb, and the frequency of SSRs appearance was 444.23 bp each. There were a total of 102 001 complete nucleotides, with the highest number of dinucleotides and the lowest number of hexanucleotides. There were 64 283 SSR's length larger than 15 bp, accounting for 67.61% of the total. There were 14 464 mixed nucleotides, accounting for 12.36% of the total SSRs. The frequency density of SSR locis on each chromosome group was in the range of 157—280 Mb, and the number of SSR locis and the length of chromosome group were highly correlated. Among the 11 chromosomes of G. jasminoides, the highest number of SSRs in Chr09 was 31 012, and the lowest number of SSRs in Chr10 was 5 360. Different SSR types repeat frequency ranged between 4—81, repeat frequency mainly concentrated in 4—20, accounting for as high as 96.30%. There were 2 429 different repeat types and 1 112 different repeat motifs in complete nucleotides, and their dominant repeat units were T, AT, AAT, AAAT, AAAAG, AAAAAT in order. The SSR sequences of G. jasminoides prefered to some extent the bases composed of A and T. Conclusion This study enriched the SSR molecular markers database of G. jasminoides, which can lay the foundation for the subsequent studies of core germplasm construction, genetic diversity analysis, variety identification and molecular marker-assisted breeding of G. jasminoides.

R286.12

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