Peng Ze, Zhao Zifan, Clevenger Josh Paul, Chu Ye, Paudel Dev, Ozias-Akins Peggy, Wang Jianping
Agronomy Department, University of Florida, Gainesville, FL, United States.
Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States.
Front Genet. 2020 Mar 24;11:222. doi: 10.3389/fgene.2020.00222. eCollection 2020.
Cultivated peanut ( L.) forms root nodules to enable a symbiotic relationship with rhizobia for biological nitrogen fixation. To understand the genetic factors of peanut nodulation, it is fundamental to genetically map and clone the genes involved in nodulation. For genetic mapping, high throughput genotyping with a large number of polymorphic markers is critical. In this study, two sets of sister recombinant inbred lines (RILs), each containing a nodulating (Nod+) and non-nodulating (Nod-) line, and their Nod+ parental lines were extensively genotyped. Several next generation sequencing (NGS) methods including target enrichment sequencing (TES), RNA-sequencing (RNA-seq), genotyping by sequencing (GBS), and the 48K Axiom SNP array, and various analysis pipelines were applied to identify single nucleotide polymorphisms (SNP) among the two sets of RILs and their parents. TES revealed the largest number of homozygous SNPs (15,947) between the original parental lines, followed by the Axiom SNP array (1,887), RNA-seq (1,633), and GBS (312). Among the five SNP analysis pipelines applied, the alignment to A/B genome followed by HAPLOSWEEP revealed the largest number of homozygous SNPs and highest concordance rate (79%) with the array. A total of 222 and 1,200 homozygous SNPs were polymorphic between the Nod+ and Nod- sister RILs and between their parents, respectively. A graphical genotype map of the sister RILs was constructed with these SNPs, which demonstrated the candidate genomic regions harboring genes controlling nodulation across the whole genome. Results of this study mainly provide the pros and cons of NGS and SNP genotyping platforms for genetic mapping in peanut, and also provide potential genetic resources to narrow down the genomic regions controlling peanut nodulation, which would lay the foundation for gene cloning and improvement of nitrogen fixation in peanut.
栽培花生（ ）形成根瘤以与根瘤菌建立共生关系进行生物固氮。为了解花生结瘤的遗传因素，对参与结瘤的基因进行遗传定位和克隆至关重要。对于遗传定位，使用大量多态性标记进行高通量基因分型至关重要。在本研究中，对两组姊妹重组自交系（RILs）进行了广泛的基因分型，每组均包含一个结瘤（Nod+）系和一个不结瘤（Nod-）系，以及它们的Nod+亲本系。应用了几种下一代测序（NGS）方法，包括目标富集测序（TES）、RNA测序（RNA-seq）、测序基因分型（GBS）和48K Axiom SNP芯片，以及各种分析流程，以鉴定两组RILs及其亲本之间的单核苷酸多态性（SNP）。TES在原始亲本系之间揭示的纯合SNP数量最多（15,947个），其次是Axiom SNP芯片（1,887个）、RNA-seq（1,633个）和GBS（312个）。在所应用的五种SNP分析流程中，与A/B基因组比对后再进行HAPLOSWEEP揭示的纯合SNP数量最多，与芯片的一致性率最高（79%）。在Nod+和Nod-姊妹RILs之间以及它们的亲本之间，分别有222个和1,200个纯合SNP具有多态性。利用这些SNP构建了姊妹RILs的图形基因型图谱，该图谱展示了全基因组中含有控制结瘤基因的候选基因组区域。本研究结果主要提供了用于花生遗传定位的NGS和SNP基因分型平台的优缺点，还提供了潜在的遗传资源以缩小控制花生结瘤的基因组区域，这将为花生基因克隆和固氮改良奠定基础。
