Liu Zhengwei, Zhu Honglian, Liu Yuping, Kuang Jing, Zhou Kai, Liang Fan, Liu Zhenhua, Wang Depeng, Ke Weidong
Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei, 430065, China.
Nextomics Biosciences Co., Ltd., Wuhan, Hubei, China.
BMC Genomics. 2016 Jun 17;17:466. doi: 10.1186/s12864-016-2781-4.
The sacred lotus (Nelumbo nucifera) is widely cultivated in China for its edible rhizomes and seeds. Traditional plant breeding methods have been used to breed cultivars with increased yields and quality of rhizomes and seeds with limited success. Currently, the available genetic maps and molecular markers in lotus are too limited to be useful for molecular genetics based breeding programs. However, the development of next-generation sequencing (NGS) technologies has enabled large-scale identification of single-nucleotide polymorphisms (SNPs) for genetic map construction. In this study, we constructed an SNP-based high-density genetic map for cultivated lotus using double digest restriction site-associated DNA sequencing (ddRADseq).
An F2 population of 96 individuals was derived from a cross between the rhizome lotus cultivar 'Juwuba' (male parent) and the seed lotus cultivar 'Mantianxing' (female parent). Genomic DNAs from this population were digested with the restriction enzymes EcoRI and MspI and then sequenced. In total, 133.65 Gb of raw data containing 1,088,935,610 pair-end reads were obtained. The coverage of reads on a reference genome was 7.2 % for the female parent, 6.56 % for the male parent, and 1.46 % for F2 individuals. From these reads, 10,753 valid SNP markers were used for genetic map construction. Finally, 791 bin markers (so-segregated adjacent SNPs treated as a bin marker), consisting of 8,971 SNP markers, were sorted into 8 linkage groups (LGs) that spanned 581.3 cM, with an average marker interval of 0.74 cM. A total of 809 genome sequence scaffolds, covering about 565.9 cM of the wild sacred lotus genome, were anchored on the genetic map, accounting for 70.6 % of the genome assembly.
This study reports the large-scale discovery of SNPs between cultivars of rhizome and seed lotus using a ddRADseq library combined with NGS. These SNPs have been used to construct the first high-density genetic map for cultivated lotus that can serve as a genomic reference and will facilitate genetic mapping of important traits in the parental cultivars.
中国广泛种植荷花（Nelumbo nucifera）以获取可食用的根茎和种子。传统的植物育种方法用于培育根茎和种子产量及品质更高的品种，但成效有限。目前，荷花中可用的遗传图谱和分子标记非常有限，无法用于基于分子遗传学的育种计划。然而，新一代测序（NGS）技术的发展使得能够大规模鉴定用于构建遗传图谱的单核苷酸多态性（SNP）。在本研究中，我们使用双酶切限制性位点关联DNA测序（ddRADseq）构建了基于SNP的栽培荷花高密度遗传图谱。
一个由96个个体组成的F2群体源自根茎型荷花品种‘巨无霸’（父本）和籽莲品种‘满天星’（母本）的杂交。用限制性内切酶EcoRI和MspI对该群体的基因组DNA进行酶切，然后测序。总共获得了133.65 Gb的原始数据，包含1,088,935,610个双端读数。母本的读数在参考基因组上的覆盖率为7.2%，父本为6.56%，F2个体为1.46%。从这些读数中，10,753个有效的SNP标记用于构建遗传图谱。最后，791个bin标记（共分离的相邻SNP视为一个bin标记），由8,971个SNP标记组成，被分为8个连锁群（LG），跨度为581.3 cM，平均标记间隔为0.74 cM。总共809个基因组序列支架，覆盖野生荷花基因组约565.9 cM，被锚定在遗传图谱上，占基因组组装的70.6%。
本研究报告了使用ddRADseq文库结合NGS在根茎型和籽莲品种之间大规模发现SNP。这些SNP已被用于构建栽培荷花的首个高密度遗传图谱，可作为基因组参考，并将有助于亲本品种重要性状的遗传定位。
