International Journal of Genomics
Volume 2016 (2016), Article ID 3602986, 6 pages
http://dx.doi.org/10.1155/2016/3602986

Research Article

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

Peng Jiang, Ping-Ping Zhang, Xu Zhang, and Hong-Xiang Ma

Provincial Key Lab for Agrobiology, Jiangsu Academy of Agricultural Sciences/Jiangsu Collaborative Innovation Center for Modern Crop Production, 50 Zhongling Street, Nanjing, Jiangsu 210014, China

Received 27 June 2016; Revised 21 July 2016; Accepted 8 August 2016

Academic Editor: Jinfa Zhang

Copyright © 2016 Peng Jiang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.

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 (Figure 2). 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 (Table 1). 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
Ningmai 4/3/Yangmai 6//88-128/Nannong P045

Ningmai 18
N18
Ningmai 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 by - 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 (Table 2), 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 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
0.45

Figure 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 (Table 3). 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 a 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 QTL Fhb1, 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.

Competing Interests

The authors declare that they have no competing interests.

Acknowledgments

This study was financially supported partially by the National Key Project for the Research and Development of China (2016YFD0100500), the Indigenous Innovation Foundation of Jiangsu Provincial Agricultural Science and Technology (CX 2021), and China Agricultural Research System Program (CARS-03).

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