欢迎访问作物学报,今天是

作物学报 ›› 2008, Vol. 34 ›› Issue (02): 217-223.doi: 10.3724/SP.J.1006.2008.00217

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

关于Mapmaker/Exp遗传作图中标记分群和排序操作技术的讨论

邢光南;赵团结;盖钧镒*   

  1. 南京农业大学大豆研究所/国家大豆改良中心/作物遗传与种质创新国家重点实验室, 江苏南京210095

  • 收稿日期:2007-04-05 修回日期:1900-01-01 出版日期:2008-02-12 网络出版日期:2008-02-12
  • 通讯作者: 盖钧镒

Application Technique of Marker Grouping and Ordering in Genetic Linkage Map Construction Using Mapmaker/Exp

XING Guang-Nan,ZHAO Tuan-Jie,GAI Jun-Yi*

  

  1. Soybean Research Institute of Nanjing Agricultural University, National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing 210095, Jiangsu, China

  • Received:2007-04-05 Revised:1900-01-01 Published:2008-02-12 Published online:2008-02-12
  • Contact: GAI Jun-Yi

摘要:

Mapmaker/Exp (3.0)是国内外广泛使用的遗传连锁数据分析软件, 在分子标记数量大时(多于500个)往往出现所绘制连锁图谱图距偏大的现象。本文从标记分群和标记排序两个遗传作图环节分析原因并概括出以下两个实施要点:(1)标记分群不应强求同一LOD值, 对特殊的连锁群可试用不同LOD值; (2)在标记排序时, 一次order命令后用ripple命令反复梳理有时并不能获得最佳排列顺序, 而应多次使用order, 每次order后用ripple反复梳理, 经反复比较才能得出最佳排列顺序, 必要时还须结合人工调整。通过大豆遗传作图实例比较了软件推荐思路2的通常用法和作者建议的新用法所构建的遗传图谱及相应QTL定位的差异, 认为新用法具有更好的效果。

关键词:

Mapmaker/Exp (3.0), 遗传连锁图谱, 作图技术, 标记分群, 标记排序

Abstract:

Mapmaker/Exp (3.0) is one of the most often used computer software packages for constructing genetic linkage map worldwide. It was found that the distances of the map constructed with the software were often exaggerated when large number of markers was involved. The present paper is to introduce our technical experiences in using Method 2 (marker number more than 500) of the software for a more reasonable linkage map. In Method 2 of Mapmaker/Exp (3.0), markers were usually grouped into linkage groups under an identical LOD value for all linkage groups; and then an “order” command followed by multiple “ripple” command was used to test the order with a window size of 5. The causes for the exaggerated map distances were found probably in two aspects in Method 2, i.e. the way of assignment of LOD value and utilization of “order” and “ripple” commands in marker grouping and marker ordering. Therefore, two innovations were taken in the application of Method 2 as: (1) different LOD values used for some specific linkage groups in addition to a common LOD value for the others; and (2) multiple “order” commands each followed with multiple “ripple” commands used for ordering markers in linkage groups, combined with some artificial adjustments when needed, for relatively higher likelihoods of the linkage groups. The innovations were used to construct a soybean genetic linkage map which showed more reasonable than that constructed with the old procedure with a better consistency to the soybean consensus map.

Key words:

Mapmaker/Exp (3.0), Genetic linkage map, Mapping technique, Marker grouping, Marker ordering

[1] 周新桐, 郭青青, 陈雪, 李加纳, 王瑞. GBS高密度遗传连锁图谱定位甘蓝型油菜粉色花性状[J]. 作物学报, 2021, 47(4): 587-598.
[2] 刘荣, 王芳, 方俐, 杨涛, 张红岩, 黄宇宁, 王栋, 季一山, 徐东旭, 李冠, 郭瑞军, 宗绪晓. 利用2个F2群体整合中国豌豆高密度SSR遗传连锁图谱[J]. 作物学报, 2020, 46(10): 1496-1506.
[3] 童治军,张谊寒,陈学军,曾建敏,方敦煌,肖炳光. 雪茄烟品种Beinhart1000-1赤星病抗性基因的QTL定位[J]. 作物学报, 2019, 45(3): 477-482.
[4] 吕品,于海峰,于志贤,张永虎,张艳芳,王婷婷,侯建华. 向日葵高密度遗传连锁图谱构建及两种水分条件下芽期性状的QTL分析[J]. 作物学报, 2017, 43(01): 19-30.
[5] 吴建忠,黄文功,康庆华,赵东升,袁红梅,于莹,刘岩,姜卫东,程莉莉,宋喜霞,赵茜,吴广文,关凤芝*. 亚麻遗传连锁图谱的构建[J]. 作物学报, 2013, 39(06): 1134-1139.
[6] 陈美霞, 祁建民, 危成林, 谢增荣, 林培清, 兰涛, 陶爱芬, 陈涛. 红麻五个质量性状在遗传连锁图谱中的初步定位[J]. 作物学报, 2011, 37(01): 165-169.
[7] 周斌,邢邯,陈受宜,盖钧镒. 大豆重组自交系群体NJRIKY遗传图谱的加密及其应用效果[J]. 作物学报, 2010, 36(1): 36-46.
[8] 刘新龙,毛钧,陆鑫,马丽,Karen Sarah AITKEN,Phillip Andrew JACKSON,蔡青,范源洪. 甘蔗SSR和AFLP分子遗传连锁图谱构建[J]. 作物学报, 2010, 36(1): 177-183.
[9] 赵丹,程须珍,王丽侠,王素华,马燕玲. 绿豆遗传连锁图谱的整合[J]. 作物学报, 2010, 36(06): 932-939.
[10] 蔡长春,柴利广,王毅,徐芳森,张俊杰,林国平. 白肋烟分子标记遗传图谱的构建及部分性状的遗传剖析[J]. 作物学报, 2009, 35(9): 1646-1654.
[11] 马红勃;祁建民;李延坤;梁景霞;王涛;兰涛;陈顺辉;陶爱芬;林荔辉;吴建梅. 烟草SRAP和ISSR分子遗传连锁图谱构建[J]. 作物学报, 2008, 34(11): 1958-1963.
[12] 陈利;张正圣;胡美纯;王威;张建;刘大军;郑靓;郑风敏;马靖. 陆地棉遗传图谱构建及产量和纤维品质性状QTL定位[J]. 作物学报, 2008, 34(07): 1199-1205.
[13] 陈旭;李新海;郝转芳;王振华;田清震;李明顺;白丽;张世煌. 玉米抗矮花叶病QTL定位[J]. 作物学报, 2005, 31(08): 983-988.
[14] 王凤格;刘贤德;王振华;张世煌;李新海;袁力行;韩晓清;李明顺. 玉米抗甘蔗花叶病毒QTL的初步研究[J]. 作物学报, 2003, 29(01): 69-74.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!