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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (6): 872-878.doi: 10.3724/SP.J.1006.2019.83067


Development of efficient KASP molecular markers based on high throughput sequencing in maize

Hai-Yan LU1,Ling ZHOU1,Feng LIN1,Rui WANG2,Feng-Ge WANG2,Han ZHAO1,*()   

  1. 1 Provincial Key Laboratory of Agrobiology / Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
    2 Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
  • Received:2018-10-07 Accepted:2019-01-19 Online:2019-06-12 Published:2019-06-12
  • Contact: Han ZHAO E-mail:zhaohan@jaas.ac.cn
  • Supported by:
    This study was supported by the National Key Research and Development Program(2017YFD0101205, 2017YFD0102005);the Jiangsu Agricultural Science and Technology Innovation Fund [CX(18)1001].(CX(18)1001)


SNP (Single Nucleotide Polymorphism) which is abundant and dispersed widely in the genome is suitable for large-scale and automated genotyping. In this study, highly polymorphic bi-allelic SNP loci were screened and 700 KASP (Kompetitive Allele Specific PCR) molecular markers were developed based on resequencing data of 205 diverse maize inbred lines. Among them, 202 KASP markers validated by 46 representative lines were further used for phylogenetic tree construction and genetic structure analysis. The validated KASP markers distributed evenly on 10 chromosomes in maize with an average PIC of 0.463 and an average MAF of 0.451. The phylogenetic tree constructed by KASP markers is highly consistent with that by re-sequencing data. In addition, the genetic similarity coefficient evaluated between KASP loci and the total SNP loci achieved 89.5% which demonstrated the availability of KASP in heterotic group division. These findings suggest that 202 KASP markers play an important role in analysis of germplasm resource, construction of genetic map, and division of heterotic group in maize.

Key words: maize, resequencing, KASP markers, germplasm

Table 1

Details of experimental materials"

205Experimental cultivars
46 cultivars for KASP
占总样本比例 Percentage
Representative inbred lines
14 6.86 4 8.69 B73, A632, 郑32, H84
B73, A632, Zheng 32, H84
改良瑞德Improved Reid 33 16.09 9 19.57 郑58, 478, 5003, 黄C, 1205A, 综3, 铁7922, K22
Zheng 58, 478, 5003, Huang C, 1205A, Zong 3, Tie 7922, K22
18 8.78 8 17.39 苏湾1611, 四路糯, CML162, DY206, CML52, Ki11, Ki3
Suwan 1611, Silunuo, CML162, DY206, CML52, Ki11, Ki3
PB 22 10.73 7 15.22 T877, 齐319, P138, 沈137, 沈135, Yu 87-1
T877, Qi 319, P138, Shen 137, Shen 135, Yu 87-1
50 24.39 6 13.04 Mo17, OH43, LH51, LH61, LH54, 龙抗11
Mo17, OH43, LH51, LH61, LH54, Longkang 11
45 21.95 9 19.57 黄早四, 昌7-2, S22, Huangyesi 3, Wu 126, 444, K12
Huangzaosi, Chang 7-2, S22, Huangyesi 3, Wu 126, 444, K12
其他Other 23 11.22 3 6.52 F2, F7

Fig. 1

Genotyping map of KASP markers a-d represent genotyping map of different KASP markers; AA: red cluster is a variety with HEX allele; GG: blue cluster is a variety with FAM allele; NTC: blank control without template."

Fig. 2

Genetic polymorphisms of 202 SNPs A: the physical location on chromosome of 202 SNPs, the numbers on the right are 202 KASP markers ID, and the numbers on the left are the physical locations, the unit is Mb; B: minimum allele frequency (MAF) and polymorphic information content (PIC) of 202 SNPs."

Fig. 3

Neighbor-joining (N-J) tree analysis A: N-J tree of 205 inbred lines based on 202 SNPs and 46 experimental materials are represented by red lines; B: N-J tree of 205 inbred lines based on 1,660,336 SNPs; Groups 1-7 represent different groups of Reid, Improved Reid, Tropic, PB, Lancaster, Sipingtou, and other latitude."

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