Genetic diversity of Poncirus and phylogenetic relationships with its relatives revealed by SSR and SNP/InDel markers

Abstract

The polymorphic markers of nuclear SSR (simple sequence repeat), SNP (single nucleotide polymorphism)/InDel (insertion-deletion length polymorphism), and cpSSR (chloroplast SSR) were used to evaluate the genetic diversity of 52 trifoliate oranges and their relatives. The two genomic DNA-based markers produced high values of PIC (polymorphic information content) at 0.45 for SNP/InDel and 0.32 for nuclear SSR, indicating that there is a large diversity of genetic variation within the trifoliate oranges. Three UPGMA (unweighted pair-group method with arithmetic means) dendrograms were generated based on the results of three marker systems. At 0.76 of coefficient, all of Poncirus accessions were clustered into one group, except the 74-1 Early Poncirus, one of the three precocious trifoliate oranges, which was placed separately into another group by nuclear SSR. At a higher coefficient, the trifoliate oranges were discriminated into 4, 6 and 6 groups by nuclear SSR (0.86), SNP/InDel (0.95), and cpSSR (0.95), respectively. The results revealed that three precocious trifoliate oranges were originated from different sources. Hubei Early Poncirus and Beibei Early Poncirus were the asexual mutants of different trifoliate oranges, and 74-1 was probably a sexual hybrid. The present study also indicated that 'Zhiwenzhou,' a diploid chimera of trifoliate orange and Satsuma is more closely related to Satsuma rather than to trifoliate orange, which is in concordance with the results of morphological observation.

A chromosome‐scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease resistance, cold tolerance and genome evolution in Citrus

“…Our study reveals a surprisingly narrow genetic base in the US germplasm collection, and indicates a strong need for further exploration and preservation of its natural genetic variation. A previous study (Zhu et al, 2015) indicates a wide genetic diversity in the native habitat of P. trifoliata in China. While still in existence, preserving and sharing this natural variation should be considered as an important item on the agenda of citrus germplasm researchers in the world to prevent the tragedy that had happened to P. polyandra, the only other species in Poncirus.…”

“…We also note that a previously published Poncirus accession (P. trifoliata Pomeroy; Wu et al, 2018) is clonally related to Little Leaf. The high degree of relatedness among the four P. trifoliata accessions indicates a very narrow genetic base for the Poncirus accessions in the US germplasm, and points to the importance of exploring additional genetic variation that exists in the native habitat of Poncirus (Zhu et al, 2015).…”