3.1 Heterozygosity rates of samples
A total of 8873 SNP loci were obtained. After collating the typing results, 6056 effective SNP loci were obtained. The ratio of the number of heterozygous markers to the total number of markers in the sample reflects the degree of homozygosity of the material. In this study, the heterozygosity rate was highest for Xinmai 18 (43.8%), with heterozygosity rates below 10%. for the other four varieties.
3.2 Genetic similarity and cluster analysis
Calculating the genetic similarity of the five variables based on loci difference revealed higher genetic similarity of Xinmai 26, Xinmai 45, and the male parent than that of the female parent. The similarity of Xinmai 26 and Jinan 17 was 0.605, and that of Xinmai 18 was 0.244. The similarity of Xinmai 45 and Jimai 20 was 0.767, and that of Xinmai 26 was 0.673. The similarity between male and female parents of Xinmai 45 was 0.463, which was higher than that of Xinmai 26 (0.246). According to the phylogenetic tree based on genetic similarity (Fig. 2), both Xinmai 26 and Xinmai 45 were closer to the male parent, and Xinmai 18 was further from the other four varieties.
3.3 Analysis of genetic loci differences between Xinmai 26, Xinmai 45, and parents
The 6056 effective SNP loci were unevenly distributed among genomes, with 2001 from Genome A, 2660 from Genome B, and 1395 from Genome D.
According to the analysis of similarities and differences between ‘Xinmai 26’ and male and female parents loci (Fig. 3), 617 loci did not differ among ‘Xinmai 18’, ‘Jinan 17’, and ‘Xinmai 26’, accounting for 10.19% of the total effective loci. The 5439 differential loci between ‘Xinmai 18’ and ‘Jinan 17’ were selected to analyze the genetic contribution of the two varieties to ‘Xinmai 2’6. The genetic contribution of ‘Jinnan 17’ to ‘Xinmai 26’ was 55.97%, which was much larger than that of ‘Xinmai 18’ (15.81%). The genetic contribution rate of ‘Jinnan 17’ exceeded 80% on seven chromosomes: 1B, 2D, 3D, 4B, 5D, 6A, and 6D. In ‘Xinmai 26’, 1535 loci were detected that were different from both male and female parents, accounting for 25.35% of all loci. The specific loci of ‘Xinmai 26’ that differed from male and female parents mapped to five chromosomes, 2A, 3B, 4A, 6B, and 7A, all of which were more than 100 (101 ~ 320); while the specific loci of Xinmai 26 that differed from male and female parents mapped to five chromosomes, 1A, 1B, 2D, 4B, and 6A, and all were less than 10 (1 ~ 6).
Figure 4 shows the numbers of similarities and differences of loci between ‘Xinmai 45’ and male and female parents. A total of 2741 loci exhibited no difference among ‘Xinmai 26’, ‘Jimai 20’, and ‘Xinmai 45’, accounting for 45.26% of all loci. There were 3315 dissimilar loci between ‘Xinmai 26’ and ‘Jimai 20’ that were selected to analyze their genetic contribution to ‘Xinmai 45’. The genetic contribution of ‘Jimai 20’ to ‘Xinmai 45’ was 57.53%, and that of ‘Xinmai 26’ to ‘Xinmai 45’ was 40.21%. ‘Xinmai 45’ had only 75 loci different from male and female parents, accounting for only 1.24% of all loci, with 51 specific loci that differed from male and female parents located in chromosome 7D. The genetic contribution rate of Jimai 20 exceeded 90% on five chromosomes, 2A, 2B, 4A, 6A, and 6B; on 4B and 7B chromosomes, the genetic contribution rate of ‘Xinmai 26’ exceeded 90%.
3.4 Genotypic map of chromosomes in Xinmai 26, Xinmai 45
According to the 15K microarray typing results of ‘Xinmai 26’, ‘Xinmai 45’, and their male and female parents, GGT2.0 was used to draw a genotypic map of ‘Xinmai 26’ and ‘Xinmai 45’ (Figs. 5 and 6).
On the 21 chromosomes of ‘Xinmai 26’ (Fig. 5), there were 130 large chromosomes with physical distance greater than 20 Mbp, 40 from female parent ‘Xinmai 26’ and 20 from male parent ‘Jinan 17’. ‘Xinmai 26’ had 14 specific fragments, and the remaining 56 fragments were not different between the three varieties. The largest numbers of large chromosomes were derived from ‘Xinmai 18’ on 3B and 5B, with five from each chromosome. There were more segments from male parent ‘Jinan 17’ on 7D and 5D, 4 and 3 segments, respectively, and no large segments from female parent ‘Xinmai 18’ on 7D. The three large segments on 1D chromosomes were all from ‘Xinmai 18’. Large segments from both male and female parents were detected on 1A, 5A, 6A, and 6D.
On the 21 chromosomes of ‘Xinmai 45’ (Fig. 6), there were 155 large chromosomes with physical distance greater than 20 Mbp, 33 from female parent ‘Xinmai 26’ and 48 from male parent ‘Jimai 20’; There were only two specific fragments, and the remaining 72 segments did not differ between the three varieties. The large segments on 4B and 7B were all from ‘Xinmai 26’, and large segments on 2A, 2B, 2D, 4A, 6A, and 6B chromosomes were all from ‘Jimai 20’. The largest proportion of identical segments of three species was found on 1B. There was one ‘Xinmai 45’ specific large fragment on both 6D and 7D,, one Xinmai 45-specific small fragment on both 4B and 5A, and no ‘Xinmai 45’ specific fragments on other chromosomes.
3.5 Chromosomal composition analysis
FISH analysis was performed on five wheat varieties, and the karyotypes of ‘Xinmai 18’, ‘Jinan 17’, ‘Xinmai 26’, ‘Jimai 20’, and ‘Xinmai 45’ are shown in Fig. 7.
No significant structural variation was found in the five varieties in comparison to the ‘Chinese spring’ karyotype. There were obvious polymorphisms in the chromosomes of groups A and B among the five varieties, and the chromosomes of group D were very consistent. The recombination of homologous chromosomes of ‘Xinmai 26’ and ‘Xinmai 45’ male and female parents of the breeding varieties can be seen in the karyotype results shown in Fig. 7. Chromosomal karyotype analysis showed that 1A, 4A, 1B, and 3B in ‘Xinmai 26’ chromosomes were from ‘Xinmai 18’, and 2A, 5A, 7A, 4B and 7B were from ‘Jinan 17’. There was no significant difference between male and female parents in the other chromosomes. For ‘Xinmai 45’, 3A, 5A, and 4D were from ‘Xinmai 26’ and 1D was from ‘Jimai 20’. There were no significant differences in the other chromosomes between male and female parents.