Yamakawa Hiromoto, Mizubayashi Tatsumi, Kitazawa Noriyuki, Yamanouchi Utako, Ando Tsuyu, Mukai Yoshiyuki, Shimosaka Etsuo, Noda Takahiro, Asano Kenji, Akai Kotaro, Katayama Kenji
Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.
Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization (NARO), 9-4 Shinseiminami, Memuro, Kasai, Hokkaido 082-0081, Japan.
Breed Sci. 2024 Dec;74(5):403-414. doi: 10.1270/jsbbs.24028. Epub 2024 Nov 23.
The progenies of polyploid crops inherit multiple sets of homoeologous chromosomes through various combinations, which impedes the identification of the quantitative trait loci (QTL) governing agronomic traits and the implementation of DNA marker-assisted breeding. Previously, we developed a whole-genome sequencing-based polyploid QTL-seq method that utilizes comprehensively extracted simplex polymorphisms for QTL mapping. Here, we verified the detection of duplex QTLs by modifying the analytical settings to explore the QTLs governing tuber flesh color and starch phosphorus content using tetraploid potato ( L.). The F progenies were obtained from a cross between 'Touya' (TY) and 'Benimaru' (BM). A single TY-derived QTL responsible for yellow flesh color was identified around a β-carotene hydroxylase gene on chromosome 3 using simplex polymorphisms, and a BM-derived QTL associated with decreased starch phosphorus content near a starch synthase II gene on chromosome 2 was detected using duplex polymorphisms. Furthermore, linked DNA markers were developed at the QTL sites. For the latter QTL, plexity-distinguishable markers were developed using quantitative PCR, fragment analysis, and amplicon sequencing. These revealed the allele dosage-dependent effect of the reduced starch phosphorus content. Thus, the polyploid QTL-seq pipeline can explore versatile QTLs beyond simplex, facilitating DNA marker-assisted breeding in various polyploid crops.
多倍体作物的后代通过各种组合继承多套部分同源染色体，这阻碍了对控制农艺性状的数量性状位点（QTL）的鉴定以及DNA标记辅助育种的实施。此前，我们开发了一种基于全基因组测序的多倍体QTL-seq方法，该方法利用全面提取的单态多态性进行QTL定位。在此，我们通过修改分析设置来验证双QTL的检测，以利用四倍体马铃薯（ ）探索控制块茎肉色和淀粉磷含量的QTL。F后代来自“Touya”（TY）和“Benimaru”（BM）之间的杂交。利用单态多态性在3号染色体上的一个β-胡萝卜素羟化酶基因附近鉴定出一个负责黄肉色的单一TY衍生QTL，利用双态多态性在2号染色体上的一个淀粉合酶II基因附近检测到一个与淀粉磷含量降低相关的BM衍生QTL。此外，在QTL位点开发了连锁DNA标记。对于后一个QTL，使用定量PCR、片段分析和扩增子测序开发了复杂性可区分标记。这些揭示了淀粉磷含量降低的等位基因剂量依赖性效应。因此，多倍体QTL-seq流程可以探索除单态之外的多种QTL，促进各种多倍体作物的DNA标记辅助育种。
