Development and Application of Transposable Element-Based Chromosomal Markers for the St Genome in Triticeae

Abstract

The St genome, originating from Pseudoroegneria (Nevski) Á. Löve, plays an important role in Triticeae. In this study, the Pseudoroegneria stipifolia genome (2n = 2x = 14, StSt) was screened to identify sequences that could be used for FISH. A total of 163 effective clones were obtained from the genomic plasmid library which was constructed by DNase I digestion of P. stipifolia nuclear genomic DNA. Analysis of these clones identified 112 with characteristics of transposable elements (TEs), 13 with characteristics of tandem repetitive sequences, 8 with characteristics of mRNA sequences, and 30 unknown sequences. Fluorescent signals were detected for 11 of 41 TE sequences on P. stipifolia chromosomes after in situ hybridization and were divided into 4 types according to signal distribution patterns: over the whole St genome chromosomes, telomere to pericentromeric regions, centromere to pericentromeric regions, and terminal regions. The affinity between St and Y genomes was studied using the 11 TE probes in 3 StStYY species. Five TE probes showed no obvious difference between subgenomes, 2 probes displayed divergence only in 2 StStYY species, and 4 probes exhibited significant differences among 3 StStYY species. These results provide a preliminary understanding of the sequence composition of the St genome and enabled 11 novel TE probes to be developed and applied.

Pseudorogneria libanotica Intraspecific Genetic Polymorphism Revealed by Fluorescence In Situ Hybridization with Newly Identified Tandem Repeats and Wheat Single-Copy Gene Probes

“…Cytogenetic and molecular markers have been used to qualitatively detect the St sub-genome in polyploids [ 16 , 25 , 26 ], however, individual St-chromosome pairs have been rarely identified in diploid Pseudoroegneria species. The newly developed FISH probe St 2 -80 in P. libanotica and transposable elements from P. stipifolia allowed the St sub-genome determination in St-containing allopolyploids [ 25 , 26 ]. Wang et al [ 21 ] processed EST-SSR and 3468 genotyping-by sequencing (GBS) markers mapping population to identify the seven homoeologous groups of the St genome in the diploid P. spicata .…”

“…Alterations in the number and distribution of tandem repeats are a crucial manifestation of intraspecific genetic variation [ 23 , 25 , 26 , 41 , 42 ]. In this study, three generated repeat probes—STlib_96, STlib_98, and STlib_117—were developed to construct the cytogenetic karyotype of P. libanotica PI 228392.…”

“…This can eliminate the karyotype inconsistency caused by different treatment methods and can act as a powerful tool for studying species variation and kindship [ 22 , 23 , 24 ]. Only a few cytogenetic markers have been employed to determine the whole St sub-genome in allopolyploids [ 25 , 26 ], however, those cytogenetic markers could not distinguish seven homoeologous chromosome groups. An attempt was made to differentiate each chromosome pair in StY genome species [ 27 ], whereas the presence and copy number of repetitive elements vary among Triticeae species.…”

Evaluation of chromosome diversity of Elymus nutans on the Qinghai‐Tibet plateau by FISH

“…TE and tandem repeat sequences were used as FISH markers to distinguish E. nutans chromosomes. S5 is a DNA transposon probe developed from the St genome (Liu et al, 2019), and AAG is a microsatellite probe widely used in Triticeae (Cuadrado et al, 2008;Cuadrado & Jouve, 2011).…”

“…Transposable elements (TEs) are a kind of dispersed repeat sequence scattered throughout the genome and interspersed with other sequences (Kubis et al, 1998). In Triticeae species such as wheat, barley, and Pseudoroegneria stipifolia , the proportion of TEs in the genome is more than 80% (Liu et al, 2019; Mascher et al, 2017; Wicker et al, 2018). In this study, we first performed FISH and GISH (Genomic in situ hybridization) analyses on four E. nutans populations from representative habitats in the QTP using a combination of TE and tandem repeat probes.…”