Development and application of genome-wide InDel markers in lettuce

TANG Dan; TU Yiyi; HUANG Zhanqian; XIAO Huiling; ZHU Xuebing; WANG Xin; CHEN Jiongjiong

doi:10.13300/j.cnki.hnlkxb.2026.02.011

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Development and application of genome-wide InDel markers in lettuce

Horticulture·Forestry | 更新时间：2026-11-05

- Development and application of genome-wide InDel markers in lettuce
- Journal of Huazhong Agricultural University Vol. 45, Issue 2, Pages: 99-112(2026)
- 作者机构：
  
  1.果蔬园艺作物种质创新与利用全国重点实验室/华中农业大学园艺林学学院，武汉430070
  2.青海省农林科学院，西宁 810016
- 作者简介：
- 基金信息：
- DOI：10.13300/j.cnki.hnlkxb.2026.02.011
  CLC： S636.2
- Received：20 February 2025，
  
  Published：15 March 2026
- 稿件说明：
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唐丹，涂艺义，黄展倩，等.莴苣全基因组InDel标记开发及应用［J］.华中农业大学学报，2026，45（2）：99‐112.

TANG Dan,TU Yiyi,HUANG Zhanqian,et al.Development and application of genome-wide InDel markers in lettuce[J].Journal of Huazhong Agricultural University,2026,45(02):99-112.
唐丹，涂艺义，黄展倩，等.莴苣全基因组InDel标记开发及应用［J］.华中农业大学学报，2026，45（2）：99‐112. DOI： 10.13300/j.cnki.hnlkxb.2026.02.011.

TANG Dan,TU Yiyi,HUANG Zhanqian,et al.Development and application of genome-wide InDel markers in lettuce[J].Journal of Huazhong Agricultural University,2026,45(02):99-112. DOI： 10.13300/j.cnki.hnlkxb.2026.02.011.

摘要

为明确莴苣主要栽培类型（结球生菜、油麦菜、莴笋）的品种遗传差异并解决同物异名问题，通过比对生菜 Salinas 与莴笋 YL1 的基因组序列，在全基因组范围鉴定出 23 901 个潜在 InDel 位点；随机选取 80 个位点设计引物，在 6 份莴笋和 6 份生菜中进行 PCR 筛选，获得 42 个稳定多态性标记，并进一步对 57 份商品品种（10 份结球生菜、24 份莴笋、23 份油麦菜）进行基因型分析。结果显示，42 个标记中 14 个适用于结球生菜区分，17 个适用于莴笋，35 个适用于油麦菜；10 份结球生菜被划分为 8 组，24 份莴笋划分为 20 组，23 份油麦菜划分为 12 组，品种间存在遗传差异及同物异名现象。结果表明，该 InDel 标记体系可直接用于莴苣品种快速鉴定与遗传背景厘清。

Abstract

The genome sequences of Salinas （lettuce） and YL1 （stem lettuce） were compared to elucidate the genetic differences among the main cultivated types of lettuce （

Lactuca sativa

） including crisphead lettuce，Youmaicai，and stem lettuce and resolve the issue of synonymy.23 901 potential InDel loci were identified across the whole genome.80 loci were randomly selected for designing primers.42 stably polymorphic markers were obtained from screening with PCR across six accessions of stem lettuce and six accessions of lettuce.57 commercial varieties including 10 crisphead lettuce，24 stem lettuce，and 23 Youmaicai were subsequently genotyped with polymorphic markers obtained.The results showed that the number of markers suitable for distinguishing crisphead lettuce，stem lettuce，and Youmaicai was 14，17，and 35 out of the 42 polymorphic markers，respectively.The 10 varieties of crisphead lettuce were classified into 8 groups，the 24 varieties of stem lettuce into 20 groups，and the 23 varieties of Youmaicai into 12 groups，meaning that there are genetic differences and synonymy among varieties.It is indicated that the developed InDel marker system can be directly used for the rapid identification and clarification of genetic background in varieties of lettuce.

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references

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