The non-random patterns of genetic variation induced by asymmetric somatic hybridization in wheat

Abstract

Background: Asymmetric somatic hybridization is an efficient crop breeding approach by introducing several exogenous chromatin fragments, which leads to genomic shock and therefore induces genome-wide genetic variation. However, the fundamental question concerning the genetic variation such as whether it occurs randomly and suffers from selection pressure remains unknown.

Results: Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Both nucleotide substitutions and indels (insertions and deletions) had lower frequencies in coding sequences than in un-translated regions. The frequencies of nucleotide substitutions and indels were both comparable between chromosomes with and without introgressed fragments. Nucleotide substitutions distributed unevenly and were preferential to indel-flanking sequences, and the frequency of nucleotide substitutions at 5'-flanking sequences of indels was obviously higher in chromosomes with introgressed fragments than in those without exogenous fragment. Nucleotide substitutions and indels both had various frequencies among seven groups of allelic chromosomes, and the frequencies of nucleotide substitutions were strongly negatively correlative to those of indels. Among three sets of genomes, the frequencies of nucleotide substitutions and indels were both heterogeneous, and the frequencies of nucleotide substitutions exhibited drastically positive correlation to those of indels.

Conclusions: Our work demonstrates that the genetic variation induced by asymmetric somatic hybridization is attributed to both whole genomic shock and local chromosomal shock, which is a predetermined and non-random genetic event being closely associated with selection pressure. Asymmetric somatic hybrids provide a worthwhile model to further investigate the nature of genomic shock induced genetic variation.

Keywords: Genetic variation; Genomic shock; Insertion and deletion; Introgression line; Nucleotide substitution.

Fig. 1

Coding region has lower SNP and indel frequencies than un-translated region. a: The total SNP and indel frequencies in 5’-UTR, CDS and 3’-UTR. The difference of the frequencies among three regions was compared using the chi-square test of fourfold cross-table analysis. 5′: 5’-UTR, 3′: 3’-UTR, C: CDS. b: The frequencies of twelve types of SNPs in 5’-UTR, CDS and 3’-UTR. c: The frequencies of indels with sizes form 1 to 10 nt in 5’-UTR, CDS and 3’-UTR. In (b) and (c), significant difference between CDS and 5′/3’-UTR (*) as well as between 5′ and 3’-UTR (#) was measured using the chi-square test of fourfold cross-table analysis

Fig. 2

The introgression of exogenous fragment does not induce stronger genetic variation of local chromosomes. a: The comparison among SNP frequencies. b: The comparison among indel frequencies. c: SNP frequencies of chromosomal arms with and without introgressed exogenous fragments. d: Indel frequencies of chromosomal arms with and without introgressed exogenous fragments. Total: all unigenes; Mapped: unigenes mapped to different chromosomal arms; Non-introgresed: unigenes mapped to chromosomal arms without exogenous fragments; Introgressed: unigenes mapped to chromosomal arms introgressed with exogenous fragments. In (a) and (b), P values were calculated using the χ² test. In (c) and (d), P values were obtained via the Student’s t-test

Fig. 3

Nucleotide substitutions are correlative to indels in chromosomes introgressed with exogenous fragments. a-c: The correlation of SNP to indel, insertion and deletion frequencies in chromosomal arms without exogenous fragments. d-f: The correlation of SNP to indel, insertion and deletion frequencies in chromosomal arms introgressed with exogenous fragments. The correlation was calculated with the Pearson correlation analysis

Fig. 4

Nucleotide substitution has higher rate close to indels. a-c: SNP frequencies of indel-flanking sequences. d-f: SNP frequencies of flanking sequences with different distance from indels. 10, 20, 30, 40: 1–10, 11–20, 21–30, 31–40 nt 3′-flanking sequences of indels; − 10, − 20, − 30, − 40: 1–10, 11–20, 21–30, 31–40 nt 5′-flanking sequences of indels. g-i: SNP frequencies of non-flanking sequences of indels. In (a)-(c) and (g)-(i), the difference significance was analyzed by the χ² test. In (d)-(f), the difference in change of SNP frequencies among intervals of flanking sequences was compared with the paired t-test. a, d and g: unigenes mapped to all chromosomal arms; b, e and h: unigenes mapped to chromosomal arms without exogenous fragments; c, f and i: unigenes mapped to chromosomal arms introgressed with exogenous fragments. In e-f: The curve was charted based on the quadratic regression equation through the regression analysis

Fig. 5

Seven groups of allelic chromosomes had similar genetic variation and exhibited negative correlation between nucleotide substitutions and indel frequencies. a, b: SNP and indel frequencies of all unigenes mapped to seven allelic chromosomes. c: The correlation between SNP and indel frequencies shown in panels (a) and (b). d-f: The relative SNP and indel frequencies of unigenes mapped to seven allelic chromosomes (d), chromosomes without introgressed fragment (e), and chromosomes with introgressed fragments (f). In a and b: The significance of difference was calculated with the the χ² test, and columns labelled with no same letter means the difference is significant (P < 0.05). In c, the correlation was calculated using the Pearson correlation analysis. In d-f, CV was coefficient of variation which was calculated as the ratio of standard deviation to mean

Fig. 6

Three genome sets had different genetic variation and exhibited positive correlation between nucleotide substitutions and indel frequencies. a, b: SNP and indel frequencies of all unigenes mapped to three genome sets. c: The correlation between SNP and indel frequencies shown in panels (a) and (b). d: The relative SNP and indel frequencies of unigenes mapped to three genome sets. e: The correlation between SNP and indel frequencies of unigenes mapped long and short arms of three genome sets. f: The relative SNP and indel frequencies of unigenes mapped to long and short arms of three genome sets. In a and b: The significance of difference was calculated with the the χ² test, and columns labelled with no same letter means the difference is significant (P < 0.05). In c and e, the correlation was calculated using the Pearson correlation analysis. In d and e, CV was coefficient of variation which was calculated as the ratio of standard deviation to mean

Fig. 7

The model of genetic variation induced by asymmetric somatic hybridization. a: Untranslated regions (UTR, non-coding sequences) have stronger genetic variation than coding sequences, and the genetic variation distributes unevenly in genes with higher frequency in indel-flanking sequences. b: The introgression of exogenous fragments induces genome-wide genetic variation by whole genomic shock and local chromosomal shock. c: The introgression of exogenous fragments induces comparable extent of genetic variation among seven allelic chromosomes but different extent among three genome sets. ▲: insertion and deletion. ●: nucleotide substitution. Red block: introgressed exogenous fragments. Blue block: whole genomic shock. Orange block: local chromosomal shock. Red curved arrows: the induction of genetic variation by the whole genomic shock, and the thickness of arrows indicates the strength of genetic variation. Blue curved arrow: the promotion of indels to nucleotide substitution at 5′-flanking sequence. Purple curved arrow: the effect of local chromosomal shock on the promotion of indels to nucleotide substitution at 5′-flanking sequence. Orange and green curved arrows: the induction of indels (orange) and nucleotide substitutions (green) by the whole genomic shock and local chromosomal shock, and the thickness of arrows indicates the strength of genetic variation. The number of dots indicates the frequency of nucleotide substitution, and the distance between dots indicated the distribution of nucleotide substitution