Genetic composition of high-quality winter wheat varieties ‘Xinmai 26’ and ‘Xinmai 45’

doi:10.21203/rs.3.rs-2954451/v1

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Genetic composition of high-quality winter wheat varieties ‘Xinmai 26’ and ‘Xinmai 45’

https://doi.org/10.21203/rs.3.rs-2954451/v1

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published 23 Sep, 2023

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High quality is an important goal of wheat breeding. Several super-strong gluten wheat varieties, e.g. ‘Xinmai 26’ and ‘Xinmai 45’, have been bred to meet the needs of the consumer market. However, the genetic composition, transmission frequency and genetic contribution of these varieties and their progeny are not clear, which is. To analyze the genetic composition of the high-quality strong gluten wheat varieties ‘Xinmai 26’ and ‘Xinmai 45’, the genetic contribution rates of male and female parents to the varieties were determined using 6056 SNP markers detected by a widely used high-throughput wheat array (15K chip). Additionally, the chromosome polymorphisms of five related wheat varieties were determined by fluorescence in situ hybridization (FISH) using four oligonucleotide probe sets. The results showed that the genetic contribution rate of ‘Jinan 17’ against ‘Xinmai 26’ was 55.97%, much higher than the 15.81% of ‘Xinmai 18’. ‘Jimai 20’ showed a genetic contribution rate of 57.53% against ‘Xinmai 45’, slightly higher than that of ‘Xinmai 26’ at 40.21%. The specific fragment differences from male and female parents were identified in both breeding varieties, and ‘Xinmai 26’ had more specific fragments that differed from male and female parents than ‘Xinmai 45’. The chromosomes of group A and group B of the five varieties were significantly polymorphic, but no chromosomal translocations or inversions were found. These promising results will allow exploration of the genetic pattern of high-quality varieties, promote breeding efficiency, and facilitate utilization of the superior traits of backbone parents for wheat quality improvement.

winter wheat

‘Xinmai 26’

‘Xinmai 45’

SNP

fluorescence in situ hybridization (FISH)

genetic composition

Wheat breeding in China has mainly focused on obtaining varieties with high yield and improved resistance. However, since the 1980s, with the improvement of the national economy, the consumer market has demanded higher quality wheat. In recent years, Chinese wheat breeding has made great progress in quality improvement (Guan et al. 2012; Wang et al. 2017), with the development of several high-quality wheat varieties that can be used as backbone parents for the selection of new varieties due to their excellent quality and significant distribution. Yu et al. (2012) used 836 Diversity Arrays Technology (DArT) markers to determine the transmission frequency and genetic contribution rate of specific marker loci in backbone parents ‘Aimengniu’ in derived offspring, and identified many chromosomal loci that were closely linked to important traits in wheat. Li et al. (2014) used 176 simple-sequence repeats (SSRs) and 683 DArT markers to analyze ‘Chuanmai 104’ and its parents. They concluded that the high spike number trait of ‘Chuanmai 104’ was derived from ‘Chuanmai 42’, the multiple spike number trait was derived from ‘Chuannong 16’ and the positive yield trait quantitative trait loci (QTL) recombination of male and female parents was the basis of high yield in ‘Chuanmai 104’. Wu et al. (2021) analyzed the genetic contribution rate of ‘Shannong 981’ and ‘Xinmai 18’ to ‘Shannong 33’ by using 53063 SNP markers detected by the wheat 55K single-nucleotide polymorphism (SNP) ‘Breeders’ array and found that the contribution of ‘Shannong 981’ to ‘Shannong 33’ was slightly greater than that of ‘Xinmai 18’.

The Xinxiang Academy of Agricultural Sciences (XAAS) is located in the high-quality wheat-producing area of northern Henan Province and developed the super-strong gluten wheat variety ‘Xinmai 26’, which was approved by the state in 2010. In the following decade, multiple breeding units developed several new high-quality super-strong gluten wheat varieties using ‘Xinmai 26’ as a backbone parent (Hua et al. 2017; Zhang et al. 2020). Among them, ‘Xinmai 45’, selected by XAAS in Henan Province, passed the national wheat variety validation in 2021, with excellent performance in quality, yield and resistance(Du et al. 2021), the flour and bread quality comparable to that of ‘Xinmai 26’. The genetic contribution of backbone varieties to their derivatives can be assessed using microarray data (Li et al. 2021; Luo et al. 2021), but few genetic analyses have been conducted on high-quality strong gluten wheat backbone parents and their derived varieties, in particular, there are few reports on genetic analysis of wheat varieties by combining FISH and gene chip hybridization. Therefore, in this study, the genetic composition of the widely grown wheat variety ‘Xinmai 26’ and its derivative ‘Xinmai 45’ was analyzed, and the transmission frequency and genetic contribution of ‘Xinmai 26’ in progeny were elucidated. The results can help to understand the genetic pattern of high-quality varieties, improve breeding efficiency, and exploit the superior traits of backbone parents for wheat quality improvement.

2.1 Materials

‘Xinmai 18’, ‘Jinan 17’, ‘Xinmai 26’, ‘Jimai 20’, and ‘Xinmai 45’ were provided by the Xinxiang Academy of Agricultural Sciences, Henan Province, China. The studied varieties and pedigrees are shown in Fig. 1.

2.2 Genomic DNA extraction and 15K microarray analysis

Fresh leaves were collected from the field in November 2020, and given to China Golden Marker (Beijing) Co., Ltd. to complete genomic DNA extraction and microarray analysis for ‘Zhongmaixin No.1’ 15K. ‘Zhongmaixin No.1’ 15K was developed by China Golden Marker (Beijing) Co., Ltd. on the platform of Affymetrix® Axiom and has evenly-distributed effective markers, high quality, and good stability, thus providing accurate genomic information.

2.3 Phylogenetic tree analysis

The NJ-tree model of Treebest software was used to establish the phylogenetic tree (Vilella et al. 2009).

2.4 Statistics of genetic contribution rate of parents to offspring varieties and genetic map

Genotyping results of offspring varieties consistent with that of the male parent were considered as contribution loci of the male parent, and genotyping results consistent with that of female parent were considered as contribution loci of the female parent. The genetic contribution rate of a particular parent to the progeny was calculated as the ratio of the number of loci contributed by that parent to the number of loci that differ between parents. The genotypic map of the progeny was constructed using GGT2.0 software (Berloo 2008).

2.5 Chromosome preparation and fluorescence in situ hybridization (FISH) karyotype analysis

Root apical cell chromosomes were prepared and cytologically compared with the reference. Oligonucleotide probes reported elsewhere were used for in situ hybridization (Huang et al. 2018); all oligonucleotides were synthesized by Shanghai Biotech Biotechnology Co., Ltd. After hybridization, the slide was washed with 2× SSC for 8 min at room temperature, rinsed with water again, and dried with air. Next, 6.5 µL of DAPI gel was added to the slide before covering with a coverslip, and the remaining gel was removed before examination under an Olympus DL72 fluorescence microscope with a SPOT Cooled Color Digital (SPOT CCD) camera. Analysis was performed using Adobe Photoshop (v6.0). For karyotype analysis, 5–10 cells of each sample were observed, one cell with complete and well-dispersed chromosomes was selected for karyotype analysis, and any overlapping chromosomes were replaced by paired chromosomes in another cell.

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 similarities of ‘Xinmai 26’, ‘Xinmai 45’, and the male parent than those 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 26’. 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 primarily mapped to five chromosomes, 2A, 3B, 4A, 6B, and 7A, with more than 100 mapping to each chromosome (101 ~ 320). The remaining loci mapped to five chromosomes, 1A, 1B, 2D, 4B, and 6A, with less than 10 to each chromosome (1 ~ 6).

Figure 4 shows the numbers of similar and different loci between ‘Xinmai 45’ and male and female parents. A total of 2741 loci (45.26% of all loci )exhibited no difference among ‘Xinmai 26’, ‘Jimai 20’, and ‘Xinmai 45’. There were 3315 dissimilar loci between ‘Xinmai 26’ and ‘Jimai 20’ that were selected for analysis of 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’ differed in 75 loci from male and female parents, accounting for only 1.24% of all loci, with 51 of these specific loci located in chromosome 7D. The genetic contribution rate of Jimai 20 exceeded 90% on five chromosomes, 2A, 2B, 4A, 6A, and 6B; the genetic contribution rate of ‘Xinmai 26’ exceeded 90% on 4B and 7B chromosomes.

3.4 Genotypic map of chromosomes in ‘Xinmai 26’ and ‘Xinmai 45’

The 15K microarray typing results of ‘Xinmai 26’, ‘Xinmai 45’, and their male and female parents were used with GGT2.0 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 chromosomal fragments at least 20 Mbp in size, 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 chromosomal segments 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, four and three segments, respectively, and no large segments from female parent ‘Xinmai 18’ on 7D. The three large segments on 1D chromosome 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 chromosomal segments at least 20 Mbp in size, 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 for the three varieties mapped to 1B. There was one ‘Xinmai 45’-specific large fragment on both 6D and 7D, one small fragment on both 4B and 5A, and none 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.

Xiao et al. (2011) studied three genetic subgroups of ‘Zhou 8425B’ and three genetic subsets of its derivatives, and obtained similar clustering results. Zhao et al. (2015) studied the original parents of ‘Kenong 9204’ and derived progeny, and the clustering results were generally consistent with the genealogical relationships. Here, the clustering clustering results in this study were inconsistent with the source of the variety and fewer varieties exhibited clustering, indicating that variety selection was mainly the result of artificial selection and different selection pressure obtained by parents. Liu et al. (2020) found that polymorphic SNP loci were most abundant in Genome B and least abundant in Genome D. Similarly in this work, the effective SNP loci were most abundant in Genome B and least abundant in Genome D.

In this study, the genetic contribution rate of ‘Xinmai 45’ male parent was slightly higher than that of female parent, similar to what was observed for male and female parents in ‘Bainong 607’ (Ma et al. 2020). Previous studies also reported a bias of offspring genetic material towards one of the parents. For instance, Xiao et al. (2011) used 921 DArT markers and 83 SSR markers and found a 67.7% genetic contribution rate of ‘Zhou 8425B’ to its derivative generation. Han et al. (2009) used 175 pairs of SSR markers and found genetic contribution rates of male and female parents to derivative varieties of the combination ‘Shengli wheat/Yanda 1817’ of 26.8% and 43.6%, respectively. Similarly, this study found a much higher genetic contribution rate of the ‘Xinmai 26’ male parent ‘Jinan 17’ compared to that of the female parent ‘Zhoumai 18’.

The genome composition, chromosomal composition, and genetic contributions of male and female parents of ‘Xinmai 26’ and ‘Xinmai 45’ wheat varieties were revealed by SNP analysis and FISH analysis at the molecular and chromosomal levels. Parents of both ‘Xinmai 26’ and ‘Xinmai 45’ showed an uneven distribution of chromosomal recombination between genes, which was consistent with the FISH results. The analysis of the breeding process of ‘Xinmai 26’ and ‘Xinmai 45’ showed the exchange of chromosomes between larger fragments, but no large-scale uniform exchange recombination across the parental genomes. In future work, the specific fragments in the bred varieties that differed from male and female parents could be the focus of a trait association study to explore the genetic basis for the formation of super parental traits.

Ethical Approval Not applicable.

Consent to Participate Not applicable.

Consent for Publication Not applicable.

Competing interests The authors declare that they have no conflict of interest.

Authors' contributions Yang LJ, Jiang ZK, and Ma HP conceived and designed the manuscript. Yang LJ and Dong YQ wrote the manuscript. Ma J, Zhang DL, Yang HF, Qi ZJ, and Li MJ participated in the experimental design, data collection, analysis of data, and preparation of the manuscript. All authors read and approved the final manuscript.

Funding This work was supported by the Modern Technology System of Agricultural Industry (CARS-3-2-34 and CARS-03-09C), the Science and Technology Major Project of Henan Province (201111110400), and the Soft Science Research Project of Xinxiang (RKX2021022).

Availability of data and materials The datasets generated during and/or analyzed in this study are available from the corresponding author on reasonable request..

Acknowledgements: We wish to thank an anonymous reviewer for his contributions in revising the manuscript.

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Table 1 Heterozygosity rates of the five varieties based on SNP markers

Sample	Xinmai 18	Jinan 17	Xinmai 26	Jimai 20	Xinmai 45
Heterozygosity rate %	43.8	1.9	1.8	2.0	1.7

Table 2 Genetic similarities of the five varieties

	Xinmai 18	Jinan 17	Xinmai 26	Jimai 20	Xinmai 45
Xinmai 18	1.000
Jinan 17	0.246	1.000
Xinmai 26	0.244	0.605	1.000
Jimai 20	0.267	0.610	0.463	1.000
Xinmai 45	0.322	0.663	0.673	0.767	1.000

No competing interests reported.

Download PDF

Journal Publication

published 23 Sep, 2023

Read the published version in Plant Molecular Biology Reporter →

Version 1

posted

You are reading this latest preprint version

Genetic composition of high-quality winter wheat varieties ‘Xinmai 26’ and ‘Xinmai 45’

Status:

Journal Publication

Version 1

Abstract

Figures

1 Introduction

2 Materials and methods

2.1 Materials

2.2 Genomic DNA extraction and 15K microarray analysis

2.3 Phylogenetic tree analysis

2.4 Statistics of genetic contribution rate of parents to offspring varieties and genetic map

2.5 Chromosome preparation and fluorescence in situ hybridization (FISH) karyotype analysis

3 Results and analysis

3.1 Heterozygosity rates of samples

3.2 Genetic similarity and cluster analysis

3.3 Analysis of genetic loci differences between ‘Xinmai 26’, ‘Xinmai 45’, and parents

3.4 Genotypic map of chromosomes in ‘Xinmai 26’ and ‘Xinmai 45’

3.5 Chromosomal composition analysis

4 Discussion and conclusions

Declarations

References

Tables

Additional Declarations

Status:

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