# Genetic Contribution of Ningmai 9 Wheat to Its Derivatives Evaluated by Using SNP Markers

Authors: Peng Jiang; Ping-Ping Zhang; Xu Zhang; Hong-Xiang Ma
Journal: International Journal of Genomics
 (2016)

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## Abstract

Founder parent usually plays an important role in wheat breeding. Ningmai 9 is a soft wheat variety with good performance in yield, quality, and resistance to wheat disease. Therefore it serves as an important commercial variety and founder parent in middle and lower Yangtze River of China. To date, 20 new cultivars have been developed from Ningmai 9 and released to wheat production in the last 10 years. In this study, the 90K iSELECT ILLUMINA chip was used to analyze the genotype of Ningmai 9 and its 17 derivatives. The genetic similarity coefficients between Ningmai 9 and its derivatives were more than 0.7 except for Yangfumai 4. Neighbor-Joining analysis showed that Yangfumai 4 had the largest genetic distance from Ningmai 9 in all derivatives. There was a great difference for the same allele ratio in either derivatives or chromosomes, though the average values of the same allele ratio in genomes A, B, and D were close to each other. The phenotypic difference in Ningmai 9, Ningmai 13, and Yangfumai 4 was consistent with their difference in genetic background by comparing previous reported QTLs. Some hot chromosome regions were found and might be used for marker assisted selection in wheat breeding.


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## Body

## 1. Introduction

Founder parents are varieties which were used to produce derivatives with desired comprehensive traits. The derivatives are more similar to founder parent rather than the mean of two parents in such traits in breeding practice, as founder parents usually have excellent comprehensive traits and high general combining ability in genetics. Genomics research found that founder parents usually contributed multiple favorable alleles to derivatives. Russell et al. (2000) analyzed the genetic diversity in 19 barley founder parents and their derivatives and found that the founder parents contributed 72% genetic variation to the derivatives [1]. Bharadwaj et al. (2002) reported that 10 Indian parents gave a genetic contribution of 72.6% to 66 soybean varieties in 1968–2000 [2]. It is very valuable to dissect the transmission efficiency and frequency of the genetic information from founder parents to their derivatives for the further utilization of founder parents in breeding.Wheat is one of the three major grain crops in the world, occupying a very important position in food security. Survey of genetic contribution of founder parent to its derivatives is important in wheat breeding. Zhuang (2003) proposed 16 founder parents which were widely used in China. Among them, a few varieties, such as Aimengniu, Xiaoyan 6, and Zhou 8425B, presented similar properties as founder parent [3]. Li et al. (2009) used 344 polymorphic simple sequence repeat (SSR) markers to screen Orofen and its 23 derivatives, and 21 SSR loci were found constant in Orofen and the derivatives [4]. “Triumph/Yanda 1817” was a core cross in northern China, and the contributions of Triumph and Yanda 1817 to their 38 derivatives were 43.6% and 26.8%, respectively [5]. Aimengniu was derived from the cross “Aifeng3//Mengxian201/Neuzucht”, and the three parents gave an average contribution of 43.2%, 35.4%, and 52.2% to its 41 derivatives [6]. All the founder parents showed a high transfer capacity of genetic information to their derivatives. However, most researches to identify the genetic contribution from parent to its derivatives in genomic level were mainly based on simple sequence repeat (SSR) markers [1, 4, 5, 7]. SSR markers were widely used in marker assisted selection, but the smaller amount of polymorphism limited their application in genetic contribution analysis. Single nucleotide polymorphism (SNP) is the most popular molecular marker at present for its genetic stability, large amount, and wide spread in genome. Some high-density gene chips based on SNP have been developed and widely used in genetic analysis of wheat, maize, rice, and so forth [8–10].Ningmai 9 is a soft wheat variety widely used in wheat production in the middle to low valley area of Yangtze River in China. As a parent, Ningmai 9 produced 20 cultivars released in the last 10 years. Two varieties derived from Ningmai 9, Ningmai 13, and Yangfumai 4 have been the major varieties in the middle to low valley area of Yangtze River in China. Either of them was planted, more than 200,000 ha each year. In this study, the 90K iSELECT ILLUMINA chip was used to screen Ningmai 9 and its 17 derivatives to show an accurate genetic contribution of Ningmai 9 to its derivatives, especially to the major varieties Ningmai 13 and Yangfumai 4 (Figure2). The results may provide a basis for the further application of Ningmai 9 in wheat breeding.


## 2. Materials and Methods

### 2.1. Plant Material and DNA Extraction

Ningmai 9 and its 17 derivatives were used as the experimental materials in this study (Table1). The DNA was extracted from fresh leaf tissue (100 mg) following a standard CTAB protocol and then diluted to 50 ng/μL for genotyping.Table 1
Name and pedigree of selected varieties.
Variety (line) Abbreviations Pedigree Ningmai 9 N9 Yangmai 6/Xifeng Ningmai 13 N13 Direct selection from Ningmai 9 Zhenmai 8 Z8 Yangmai 158/Ningmai 9 Nannong 0686 Nan0686 MV964091/Ningmai 9 Yangmai 18 Y18 Ningmai9∗4/3/Yangmai 158∗6//88-128/Nannong P045 Ningmai 18 N18 Ningmai9∗2//Ningmai 9/Yangmai 10 Ning 9-78 N9-78 Direct selection from Ningmai 9 Ning 9-44 N9-44 Direct selection from Ningmai 9 Ning 9-11 N9-11 Direct selection from Ningmai 9 Ningmai 16 N16 Ningmai 8/Ningmai 9 Ning 0311 N0311 Ningmai 8/Ningmai 9 Ning 0320 N0320 Ningmai 8/Ningmai 9 Ning 0331 N0331 Ningmai 8/Ningmai 9 Ning 0417 N0417 Ningmai 8/Ningmai 9 Ning 0422 N0422 Ningmai 8/Ningmai 9 Ning 0798 N0798 Ningmai 9 large/Yangfu 9798//Sumai 6 Yangfumai 4 YF4 Mutant induced byCo60-γ radiation from Ningmai 8/Ningmai 9 Shengxuan 6 S6 Ningmai 8/Ningmai 9


### 2.2. SNP Assay

Genotyping procedure for the 90K iSELECT ILLUMINA chip was performed as described by Wang et al. (2014) [11] at the USDA Genotyping Center. Genotypic clusters for every SNP were determined using the manual option of Genome Studio version 1.9.4 with the polyploid clustering version 1.0.0 (Illumina), on the basis of the data from all of the described genotypes. A total of 81587 SNPs including BS, Bob White, CAP, and D contig were obtained.


### 2.3. Data Analysis

6904 SNPs out of 81587 SNPs were selected according to 3 filtering conditions: there was no missing data, there was difference among the materials, and there was an ensured position on the chromosome. The 6904 screened SNPs were used for further analysis. Excel 2007 was used for data processing and statistic analyzing. NTSYSpc version 2.10t was used to calculate genetic similarity coefficients (GSCs), and Neighbor-Joining tree was constructed by MEGA 6.0 [12].


## 2.1. Plant Material and DNA Extraction

Ningmai 9 and its 17 derivatives were used as the experimental materials in this study (Table1). The DNA was extracted from fresh leaf tissue (100 mg) following a standard CTAB protocol and then diluted to 50 ng/μL for genotyping.Table 1
Name and pedigree of selected varieties.
Variety (line) Abbreviations Pedigree Ningmai 9 N9 Yangmai 6/Xifeng Ningmai 13 N13 Direct selection from Ningmai 9 Zhenmai 8 Z8 Yangmai 158/Ningmai 9 Nannong 0686 Nan0686 MV964091/Ningmai 9 Yangmai 18 Y18 Ningmai9∗4/3/Yangmai 158∗6//88-128/Nannong P045 Ningmai 18 N18 Ningmai9∗2//Ningmai 9/Yangmai 10 Ning 9-78 N9-78 Direct selection from Ningmai 9 Ning 9-44 N9-44 Direct selection from Ningmai 9 Ning 9-11 N9-11 Direct selection from Ningmai 9 Ningmai 16 N16 Ningmai 8/Ningmai 9 Ning 0311 N0311 Ningmai 8/Ningmai 9 Ning 0320 N0320 Ningmai 8/Ningmai 9 Ning 0331 N0331 Ningmai 8/Ningmai 9 Ning 0417 N0417 Ningmai 8/Ningmai 9 Ning 0422 N0422 Ningmai 8/Ningmai 9 Ning 0798 N0798 Ningmai 9 large/Yangfu 9798//Sumai 6 Yangfumai 4 YF4 Mutant induced byCo60-γ radiation from Ningmai 8/Ningmai 9 Shengxuan 6 S6 Ningmai 8/Ningmai 9


## 2.2. SNP Assay

Genotyping procedure for the 90K iSELECT ILLUMINA chip was performed as described by Wang et al. (2014) [11] at the USDA Genotyping Center. Genotypic clusters for every SNP were determined using the manual option of Genome Studio version 1.9.4 with the polyploid clustering version 1.0.0 (Illumina), on the basis of the data from all of the described genotypes. A total of 81587 SNPs including BS, Bob White, CAP, and D contig were obtained.


## 2.3. Data Analysis

6904 SNPs out of 81587 SNPs were selected according to 3 filtering conditions: there was no missing data, there was difference among the materials, and there was an ensured position on the chromosome. The 6904 screened SNPs were used for further analysis. Excel 2007 was used for data processing and statistic analyzing. NTSYSpc version 2.10t was used to calculate genetic similarity coefficients (GSCs), and Neighbor-Joining tree was constructed by MEGA 6.0 [12].


## 3. Results

### 3.1. Genetic Relationship among Ningmai 9 and Its Derivatives

All the genetic similarity coefficients (GSCs) between Ningmai 9 and its derivatives were more than 0.7 except for Yangfumai 4 (Table2), indicating that Ningmai 9 had a high rate of genetic transmission. Ning 9-44 had the highest GSC (0.98) with Ningmai 9, and the lowest GSC was observed between Nannong 0686 and Yangfumai 4 (0.36). Neighbor-Joining analysis presented similar results (Figure 1). Ningmai 9 and Ning 9-44 clustered together. Yangfumai 4 was clustered at the largest genetic distance. The largest genetic distance was between Nannong 0686 and Yangfumai 4. Neighbor-Joining analysis also reflected the pedigrees to some extent. Ningmai 13, Ning 9-78, Ning 9-44, and Ning 9-11 were all directly selected from Ningmai 9, and they clustered together. Both Yangmai 18 and Ningmai 18 obtained genetic information from Ningmai 9 and Yangmai 158 (Yangmai 10 was derived from Yangmai 158), and Ningmai 16 and Shengxuan 6 were both derived from the cross Ningmai 8/Ningmai 9. Yangfumai 4 was the farthest from the other materials since it was a Co-γ60 radiated mutant from the hybrid seeds of the cross Ningmai 8/Ningmai 9.Table 2
Genetic similarity coefficient among N9 and its derivatives.
N9 N13 Z8 Nan0686 Y18 N18 N9-78 N9-44 N9-11 N16 N0311 N0320 N0331 N0417 N0422 N0798 YF4 N13 0.96 Z8 0.78 0.77 Nan0686 0.71 0.69 0.61 Y18 0.86 0.84 0.73 0.75 N18 0.89 0.87 0.72 0.75 0.94 N9-78 0.96 0.97 0.77 0.70 0.85 0.87 N9-44 0.98 0.96 0.78 0.71 0.86 0.89 0.96 N9-11 0.95 0.95 0.77 0.69 0.85 0.87 0.96 0.95 N16 0.85 0.83 0.73 0.74 0.89 0.89 0.83 0.84 0.82 N0311 0.76 0.77 0.77 0.61 0.76 0.75 0.76 0.77 0.76 0.76 N0320 0.85 0.83 0.75 0.72 0.87 0.88 0.83 0.84 0.83 0.89 0.80 N0331 0.80 0.78 0.74 0.66 0.85 0.84 0.78 0.80 0.79 0.83 0.77 0.84 N0417 0.73 0.74 0.69 0.60 0.73 0.73 0.73 0.73 0.73 0.75 0.75 0.79 0.78 N0422 0.82 0.82 0.71 0.70 0.83 0.83 0.82 0.83 0.82 0.86 0.78 0.85 0.79 0.75 N0798 0.78 0.78 0.75 0.67 0.73 0.73 0.78 0.78 0.77 0.78 0.71 0.79 0.75 0.72 0.75 YF4 0.43 0.45 0.44 0.36 0.45 0.44 0.44 0.43 0.44 0.44 0.51 0.47 0.48 0.47 0.46 0.43 S6 0.86 0.84 0.73 0.74 0.91 0.91 0.84 0.86 0.84 0.90 0.75 0.86 0.83 0.73 0.87 0.74 0.45Figure 1
Dendrogram of Ningmai 9 and its derivatives based on Neighbor-Joining analysis. The genetic distance of Yangfumai 4 was very large and broken down with dashed line.Figure 2
Genetic contribution of Ningmai 9 to Ningmai 13 and Yangfumai 4. White regions are identical sections in Ningmai 9, Ningmai 13, and Yangfumai 4; red regions are different sections among Ningmai 9, Ningmai 13, and Yangfumai 4; blue regions represent different section of Ningmai 13, and gray regions represent different section of Yangfumai 4; and black regions are identical sections between Ningmai 13 and Yangfumai 4, but different from Ningmai 9.


### 3.2. Distribution of Genetic Information of Ningmai 9 on 21 Chromosomes of Its Derivatives

The means of SNPs on each chromosome in genomes A, B, and D were 411, 496, and 80, respectively. There was great difference for the same allele ratios (SAR) in either derivatives or chromosomes. Taking chromosome 1A as an example, SAR between Ningmai 9 and Ning 9-78 reached 100%, while SAR was only 28% between Ningmai 9 and Yangfumai 4 (Table3). The average values of SAR on different chromosomes were different, which ranged from 62% on chromosome 4D to 91% on chromosome 6D. The SAR values of 18 chromosomes in all 21 chromosomes ranged from 70% to 90%; however, the average values of SAR in genomes A, B, and D were close to each other.Table 3
Same allele ratios (SAR) between Ningmai 9 and its derivatives on 21 chromosomes (%).
SNPs N13 Z8 Nan0686 Y18 N18 N9-78 N9-44 N9-11 N16 N0311 N0320 N0331 N0417 N0422 N0798 YF4 S6 Mean 1A 460 99 57 76 93 99 100 100 99 76 58 90 80 86 69 99 28 76 82 2A 440 98 80 78 98 93 99 99 99 98 79 98 88 79 80 83 40 80 87 3A 343 99 50 92 95 92 95 96 97 90 59 72 58 63 95 50 28 95 78 4A 350 95 90 67 93 92 99 100 99 93 86 93 75 47 79 92 27 90 83 5A 414 97 94 71 79 80 97 98 96 85 76 79 79 83 88 90 54 88 84 6A 460 97 97 27 76 96 97 97 97 96 94 95 95 95 95 95 66 95 89 7A 407 94 81 66 58 64 93 100 87 62 56 61 55 50 60 85 29 55 68 Mean 411 97 78 68 85 88 97 98 96 86 73 84 76 72 81 85 39 83 82  1B 757 99 98 87 90 89 98 99 98 87 86 85 89 85 86 87 77 89 90 2B 481 99 69 72 78 89 97 97 97 76 68 73 77 60 74 70 43 73 77 3B 349 88 78 59 76 83 87 89 87 80 79 89 78 69 79 72 29 86 77 4B 178 51 49 87 72 90 52 90 37 88 54 87 62 31 61 30 36 88 63 5B 671 95 80 56 82 82 95 96 96 77 73 80 83 80 80 66 20 83 78 6B 537 99 76 90 95 98 99 100 99 97 92 96 78 81 95 89 39 97 89 7B 500 98 51 70 98 98 98 98 98 87 80 86 94 75 95 74 49 98 85 Mean 496 90 71 74 84 90 89 96 87 85 76 85 80 69 81 70 42 88 80  1D 122 98 78 55 81 81 100 99 98 68 70 68 64 69 66 64 53 81 76 2D 219 96 90 74 95 93 98 95 97 97 91 94 89 55 97 39 75 97 86 3D 41 100 98 78 71 93 78 100 76 63 73 73 71 63 76 83 27 71 76 4D 24 100 54 29 54 54 100 100 58 54 54 58 54 50 54 71 46 54 62 5D 65 95 85 48 94 80 95 97 95 85 83 94 94 75 82 91 60 95 85 6D 44 100 98 95 95 98 100 100 100 93 91 91 98 77 95 89 30 93 91 7D 42 100 86 67 86 90 93 100 93 71 71  74 76 79 93 45 90 82 Mean 80 98 84 64 82 84 95 99 88 76 76 81 78 67 78 76 48 83 80  Overall mean 329 95 78 69 84 87 94 98 91 82 75 83 78 69 80 77 43 85


### 3.3. Genetic Contribution of Ningmai 9 to Ningmai 13 and Yangfumai 4

Ningmai 13 and Yangfumai 4 were both derivatives of Ningmai 9, but there was great difference in the genetic background, and the GSC between them was only 0.45. Ningmai 13 was more similar to Ningmai 9 than Yangfumai 4 was. Few variations were observed on chromosomes of Ningmai 13, especially on chromosomes 3D, 4D, 6D, and 7D, which were fully consistent with Ningmai 9, while variable regions were over 50% on most chromosomes of Yangfumai 4 in comparison with the alleles in Ningmai 9. The regions where Ningmai 13 and Yangfumai 4 shared the same variation were observed on chromosomes 3B, 4B, and 5A, while the regions with different variations between Ningmai 13 and Yangfumai 4 were presented on chromosomes 1A, 1B, and 4A.


## 3.1. Genetic Relationship among Ningmai 9 and Its Derivatives

All the genetic similarity coefficients (GSCs) between Ningmai 9 and its derivatives were more than 0.7 except for Yangfumai 4 (Table2), indicating that Ningmai 9 had a high rate of genetic transmission. Ning 9-44 had the highest GSC (0.98) with Ningmai 9, and the lowest GSC was observed between Nannong 0686 and Yangfumai 4 (0.36). Neighbor-Joining analysis presented similar results (Figure 1). Ningmai 9 and Ning 9-44 clustered together. Yangfumai 4 was clustered at the largest genetic distance. The largest genetic distance was between Nannong 0686 and Yangfumai 4. Neighbor-Joining analysis also reflected the pedigrees to some extent. Ningmai 13, Ning 9-78, Ning 9-44, and Ning 9-11 were all directly selected from Ningmai 9, and they clustered together. Both Yangmai 18 and Ningmai 18 obtained genetic information from Ningmai 9 and Yangmai 158 (Yangmai 10 was derived from Yangmai 158), and Ningmai 16 and Shengxuan 6 were both derived from the cross Ningmai 8/Ningmai 9. Yangfumai 4 was the farthest from the other materials since it was a Co-γ60 radiated mutant from the hybrid seeds of the cross Ningmai 8/Ningmai 9.Table 2
Genetic similarity coefficient among N9 and its derivatives.
N9 N13 Z8 Nan0686 Y18 N18 N9-78 N9-44 N9-11 N16 N0311 N0320 N0331 N0417 N0422 N0798 YF4 N13 0.96 Z8 0.78 0.77 Nan0686 0.71 0.69 0.61 Y18 0.86 0.84 0.73 0.75 N18 0.89 0.87 0.72 0.75 0.94 N9-78 0.96 0.97 0.77 0.70 0.85 0.87 N9-44 0.98 0.96 0.78 0.71 0.86 0.89 0.96 N9-11 0.95 0.95 0.77 0.69 0.85 0.87 0.96 0.95 N16 0.85 0.83 0.73 0.74 0.89 0.89 0.83 0.84 0.82 N0311 0.76 0.77 0.77 0.61 0.76 0.75 0.76 0.77 0.76 0.76 N0320 0.85 0.83 0.75 0.72 0.87 0.88 0.83 0.84 0.83 0.89 0.80 N0331 0.80 0.78 0.74 0.66 0.85 0.84 0.78 0.80 0.79 0.83 0.77 0.84 N0417 0.73 0.74 0.69 0.60 0.73 0.73 0.73 0.73 0.73 0.75 0.75 0.79 0.78 N0422 0.82 0.82 0.71 0.70 0.83 0.83 0.82 0.83 0.82 0.86 0.78 0.85 0.79 0.75 N0798 0.78 0.78 0.75 0.67 0.73 0.73 0.78 0.78 0.77 0.78 0.71 0.79 0.75 0.72 0.75 YF4 0.43 0.45 0.44 0.36 0.45 0.44 0.44 0.43 0.44 0.44 0.51 0.47 0.48 0.47 0.46 0.43 S6 0.86 0.84 0.73 0.74 0.91 0.91 0.84 0.86 0.84 0.90 0.75 0.86 0.83 0.73 0.87 0.74 0.45Figure 1
Dendrogram of Ningmai 9 and its derivatives based on Neighbor-Joining analysis. The genetic distance of Yangfumai 4 was very large and broken down with dashed line.Figure 2
Genetic contribution of Ningmai 9 to Ningmai 13 and Yangfumai 4. White regions are identical sections in Ningmai 9, Ningmai 13, and Yangfumai 4; red regions are different sections among Ningmai 9, Ningmai 13, and Yangfumai 4; blue regions represent different section of Ningmai 13, and gray regions represent different section of Yangfumai 4; and black regions are identical sections between Ningmai 13 and Yangfumai 4, but different from Ningmai 9.


## 3.2. Distribution of Genetic Information of Ningmai 9 on 21 Chromosomes of Its Derivatives

The means of SNPs on each chromosome in genomes A, B, and D were 411, 496, and 80, respectively. There was great difference for the same allele ratios (SAR) in either derivatives or chromosomes. Taking chromosome 1A as an example, SAR between Ningmai 9 and Ning 9-78 reached 100%, while SAR was only 28% between Ningmai 9 and Yangfumai 4 (Table3). The average values of SAR on different chromosomes were different, which ranged from 62% on chromosome 4D to 91% on chromosome 6D. The SAR values of 18 chromosomes in all 21 chromosomes ranged from 70% to 90%; however, the average values of SAR in genomes A, B, and D were close to each other.Table 3
Same allele ratios (SAR) between Ningmai 9 and its derivatives on 21 chromosomes (%).
SNPs N13 Z8 Nan0686 Y18 N18 N9-78 N9-44 N9-11 N16 N0311 N0320 N0331 N0417 N0422 N0798 YF4 S6 Mean 1A 460 99 57 76 93 99 100 100 99 76 58 90 80 86 69 99 28 76 82 2A 440 98 80 78 98 93 99 99 99 98 79 98 88 79 80 83 40 80 87 3A 343 99 50 92 95 92 95 96 97 90 59 72 58 63 95 50 28 95 78 4A 350 95 90 67 93 92 99 100 99 93 86 93 75 47 79 92 27 90 83 5A 414 97 94 71 79 80 97 98 96 85 76 79 79 83 88 90 54 88 84 6A 460 97 97 27 76 96 97 97 97 96 94 95 95 95 95 95 66 95 89 7A 407 94 81 66 58 64 93 100 87 62 56 61 55 50 60 85 29 55 68 Mean 411 97 78 68 85 88 97 98 96 86 73 84 76 72 81 85 39 83 82  1B 757 99 98 87 90 89 98 99 98 87 86 85 89 85 86 87 77 89 90 2B 481 99 69 72 78 89 97 97 97 76 68 73 77 60 74 70 43 73 77 3B 349 88 78 59 76 83 87 89 87 80 79 89 78 69 79 72 29 86 77 4B 178 51 49 87 72 90 52 90 37 88 54 87 62 31 61 30 36 88 63 5B 671 95 80 56 82 82 95 96 96 77 73 80 83 80 80 66 20 83 78 6B 537 99 76 90 95 98 99 100 99 97 92 96 78 81 95 89 39 97 89 7B 500 98 51 70 98 98 98 98 98 87 80 86 94 75 95 74 49 98 85 Mean 496 90 71 74 84 90 89 96 87 85 76 85 80 69 81 70 42 88 80  1D 122 98 78 55 81 81 100 99 98 68 70 68 64 69 66 64 53 81 76 2D 219 96 90 74 95 93 98 95 97 97 91 94 89 55 97 39 75 97 86 3D 41 100 98 78 71 93 78 100 76 63 73 73 71 63 76 83 27 71 76 4D 24 100 54 29 54 54 100 100 58 54 54 58 54 50 54 71 46 54 62 5D 65 95 85 48 94 80 95 97 95 85 83 94 94 75 82 91 60 95 85 6D 44 100 98 95 95 98 100 100 100 93 91 91 98 77 95 89 30 93 91 7D 42 100 86 67 86 90 93 100 93 71 71  74 76 79 93 45 90 82 Mean 80 98 84 64 82 84 95 99 88 76 76 81 78 67 78 76 48 83 80  Overall mean 329 95 78 69 84 87 94 98 91 82 75 83 78 69 80 77 43 85


## 3.3. Genetic Contribution of Ningmai 9 to Ningmai 13 and Yangfumai 4

Ningmai 13 and Yangfumai 4 were both derivatives of Ningmai 9, but there was great difference in the genetic background, and the GSC between them was only 0.45. Ningmai 13 was more similar to Ningmai 9 than Yangfumai 4 was. Few variations were observed on chromosomes of Ningmai 13, especially on chromosomes 3D, 4D, 6D, and 7D, which were fully consistent with Ningmai 9, while variable regions were over 50% on most chromosomes of Yangfumai 4 in comparison with the alleles in Ningmai 9. The regions where Ningmai 13 and Yangfumai 4 shared the same variation were observed on chromosomes 3B, 4B, and 5A, while the regions with different variations between Ningmai 13 and Yangfumai 4 were presented on chromosomes 1A, 1B, and 4A.


## 4. Discussion

Ningmai 9 is a soft wheat variety with high yield, wide adaptation, moderate resistance to Fusarium head blight and sharp eye spot, and high resistance to wheat yellow mosaic virus and serves as important parent in middle and lower valley of Yangtze River in China. Twenty new wheat cultivars have been developed from Ningmai 9 in the last 10 years. Founder parents easily produce varieties because of their excellent comprehensive characters and high genetic combining ability [3]. From the genomic point of view, the founder parent has favorable alleles associated with comprehensive traits. Su et al. (2006) identified 39 QTLs related with number of tillers and phosphorus absorption efficiency with a double haploid population from Lovrin 10/Chinese Spring, and 15 of them were from Lovrin 10 [13]; Christopher et al. (2007) discovered a few high frequency alleles related with some important traits with a wheat pedigree based on Cook and a barley pedigree based on crosses between Triumph and Koru [14]; Ma et al. (2007) used a double haploid population from Nanda 2419/Wangshuibai to identify a few QTLs controlling ear length and ear density from Nanda 2419 [15]. Yao et al. (2012) identified the high combining ability of Ningmai 9 in yield, quality, and resistance and the successful application in wheat breeding [16]. In this study, we analyzed the genotype of Ningmai 9 and its derivatives by using 90K iSELECT ILLUMINA chip and found that the GSCs between Ningmai 9 and its derivatives were mostly over 0.7 except for Yangfumai 4, which was significantly higher than its theoretical expectation, indicating a high rate of genetic transmission in Ningmai 9.Ningmai 16, Shengxuan 6, Ning 0311, Ning 0417, and Yangfumai 4 were derived from the same cross of Ningmai 8/Ningmai 9. Theoretically, the varieties from the same cross combination may have high GSCs and close genetic distance in the dendrogram based on Neighbor-Joining analysis. Ningmai 16 and Shengxuan 6 confirmed the theory, whereas other derivatives from the same cross were relatively far apart, such as Ning 0311 and Ning 0417, which means that the selection by breeders was a crucial factor affecting the genetic background of offspring from the same cross. Yangfumai 4 was aCo-γ60 radiated mutant of hybrid seeds from the same cross and had the lowest GSC with Ningmai 9, which indicated that radiation was an effective way to create some novel genetic variation.Backcross can improve the genetic proportion of the recurrent parent significantly. Yangmai 18 and Ningmai 18 experienced 4 and 2 rounds of backcross with Ningmai 9, respectively, and their GSCs with Ningmai 9 were only second to the derivatives directly selected from Ningmai 9.Ningmai 13 is the most popular soft wheat variety, and Yangfumai 4 is the most popular hard wheat in middle and lower Yangtze River of China now. Ningmai 13 inherited the features of good soft wheat quality, effective tillers, and FHB resistance from Ningmai 9 and improved lodging resistance and thousand kernel weight (TKW). Yangfumai 4 presented a distinct difference from Ningmai 9 and had a hard wheat quality with high to medium gluten content, big ear, and large size kernel. Ningmai 13 and Yangfumai 4 both had high resistance to wheat yellow mosaic virus as Ningmai 9. Ningmai 9 possessed the wheat yellow mosaic virus resistant QTL with the same allele on chromosome 2DL and 3BS as previous reports [17, 18]. Ningmai 13 and Yangfumai 4 had the identical alleles on the chromosome regions with Ningmai 9. For the resistance to Fusarium head blight (FHB), Ningmai 9 had the major QTLFhb1, which was the most important FHB resistant QTL on chromosome 3BS [19]. Ningmai 13 and Yangfumai 4 also had the same chromosome region as in Ningmai 9 and performed the resistance to FHB. Many QTLs controlling grain number per ear, ear weight, and ear length had been reported on chromosomes 2A, 2B, 2D, 4A, 5A, 5D, and 6B [20–22], where most variations were only observed in Yangfumai 4. The QTLs controlling thousand kernel weight were identified on chromosomes 2A, 2D, 3B, 4B, 6A, 7A, and 7B [21, 23], and those controlling lodging resistance were discovered on chromosomes 2A, 2D, 3B, 5A, 5B, and 5D [24–26], on which Ningmai 13 and Yangfumai 4 both presented same alleles. These chromosome regions may contain QTLs associated with thousand kernel weight and lodging resistance. Such hot chromosome regions might be used for marker assisted selection in wheat breeding.In the study, we validated that Ningmai 9 is a founder parent on genomic level. The derivative varieties inherited a high proportion of the genetic background from Ningmai 9, especially on some hot variation regions associated with desired comprehensive characters.



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*Source: 3602986-2016-08-29.xml*