Ting Ngoot-Chin, Jansen Johannes, Mayes Sean, Massawe Festo, Sambanthamurthi Ravigadevi, Ooi Leslie Cheng-Li, Chin Cheuk Weng, Arulandoo Xaviar, Seng Tzer-Ying, Alwee Sharifah Shahrul Rabiah Syed, Ithnin Maizura, Singh Rajinder
Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), No, 6, Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia.
BMC Genomics. 2014 Apr 27;15(1):309. doi: 10.1186/1471-2164-15-309.
Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest.
A 4.5 K customized oil palm SNP array was developed using the Illumina Infinium platform. The SNPs and 252 SSRs were genotyped on two mapping populations, an intraspecific cross with 87 palms and an interspecific cross with 108 palms. Parental maps with 16 linkage groups (LGs), were constructed for the three fruit forms of E. guineensis (dura, pisifera and tenera). Map resolution was further increased by integrating the dura and pisifera maps into an intraspecific integrated map with 1,331 markers spanning 1,867 cM. We also report the first map of a Colombian E. oleifera, comprising 10 LGs with 65 markers spanning 471 cM. Although not very dense due to the high level of homozygosity in E. oleifera, the LGs were successfully integrated with the LGs of the tenera map. Direct comparison between the parental maps identified 603 transferable markers polymorphic in at least two of the parents. Further analysis revealed a high degree of marker transferability covering 1,075 cM, between the intra- and interspecific integrated maps. The interspecific cross displayed higher segregation distortion than the intraspecific cross. However, inclusion of distorted markers in the genetic maps did not disrupt the marker order and no map expansion was observed.
The high density SNP and SSR-based genetic maps reported in this paper have greatly improved marker density and genome coverage in comparison with the first reference map based on AFLP and SSR markers. Therefore, it is foreseen that they will be more useful for fine mapping of QTLs and whole genome association mapping studies in oil palm.
油棕是一种重要的多年生油料作物，其选择周期极长，为10至12年。因此，任何能够加速其遗传改良进程的工具，如分子标记辅助育种，都非常宝贵。此前，基于AFLP、RFLP和SSR标记构建了遗传连锁图谱，并鉴定了脂肪酸组成和产量构成因素的数量性状位点（QTL）。不同遗传背景杂交组合的高密度遗传图谱是研究油棕遗传学不可或缺的工具。它们也有助于进行比较图谱分析，以鉴定与感兴趣性状紧密连锁的标记。
利用Illumina Infinium平台开发了一个包含4500个位点的定制油棕单核苷酸多态性（SNP）芯片。在两个作图群体上对这些SNP和252个SSR进行了基因分型，一个是有87株棕榈的种内杂交群体，另一个是有108株棕榈的种间杂交群体。针对油棕的三种果实类型（厚壳种、薄壳种和 Tenera 种）构建了具有16个连锁群（LG）的亲本图谱。通过将厚壳种和薄壳种的图谱整合到一个包含1331个标记、跨度为1867厘摩（cM）的种内整合图谱中，进一步提高了图谱分辨率。我们还报道了首个哥伦比亚油棕的图谱，该图谱包含10个LG，有65个标记，跨度为471 cM。尽管由于油棕的纯合度较高导致该图谱密度不是很高，但这些LG已成功与Tenera种图谱的LG整合。亲本图谱之间的直接比较确定了603个可转移标记，这些标记在至少两个亲本中具有多态性。进一步分析显示，种内和种间整合图谱之间有1075 cM的标记具有高度可转移性。种间杂交显示出比种内杂交更高的分离畸变。然而，在遗传图谱中纳入畸变标记并未扰乱标记顺序，也未观察到图谱扩展。
与基于AFLP和SSR标记的首个参考图谱相比，本文报道的基于高密度SNP和SSR的遗传图谱极大地提高了标记密度和基因组覆盖范围。因此，可以预见，它们将更有助于油棕中QTL的精细定位和全基因组关联作图研究。
