Abstract
Cultivated peanut (Arachis hypogaea 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 Arachis2 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 Arachis2 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.
Highlights
Peanut (Arachis hypogaea L.) is one of the most important oilseed crops grown worldwide
Only a small proportion (14 out of 57, 24.56%) of the SNPs from M2 overlapped with M4, both revealed a high validation rate for homozygous SNPs (Figure 2C). This was observed for RNA-seq data, in which only 4 (12.12%) out of 33 SNPs from M2 were covered by M4 (Figure 2D). These results showed that M2 and M4/M5 were able to identify different portions of true homozygous SNPs out of the existing true polymorphisms
We mainly focused on identifying the polymorphic regions between two pairs of sister recombinant inbred lines (RILs), E4 & E5, as well as E6 & E7, which are near-isogenic lines
Summary
Peanut (Arachis hypogaea L.) is one of the most important oilseed crops grown worldwide. Non-nodulating (Nod-) peanut plants, first reported by Gorbet and Burton (1979), are important materials for dissecting the genetic factors of peanut nodulation. The Nod- peanut plants were first identified in an F3 population from a cross between two nodulating (Nod+) genotypes 487A-4-1-2 and PI 262090 (Gorbet and Burton, 1979). A transcriptome study using root samples from two sets of recombinant inbred lines (RILs) with Nod+ and Nod− phenotype revealed hundreds of differentially expressed genes (DEGs) upon infection with rhizobia (Peng et al, 2017a). The same materials were morphologically and genetically characterized to initiate studies on peanut nodulation genes (Peng et al, 2018). With the aid of generation sequencing (NGS) technologies, the map density could be further improved
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
