Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)


Biology and Microbiology

First Advisor

Yang Yen


GBS, maize, perennialism, SNP, LOD


Developing perennial grain crops is an effective and crucial way to prevent soil erosion caused by conventional agriculture of using annual crops while meeting the increasing need of global food demand. We hypothesized that the regrowth in Zea might be controlled by two dominant complementary genes. F1 hybrids were created by crossing Zea diploperennis Iltis, Doebley & R. Guzman with annual Zea mays L. ssp. mays inbred line B73. A Total of 134 F2 plants derived from nine F1 were planted and phenotyped. A subpopulation of 94 F2 plants were genotyped with Genotype-by- Sequencing (GBS) and called 10,431 SNPs after filtering. A total number of 946 SNPs were then found related to regrowth by chi-square goodness of fit test P(χ2) > 0.05. Two chromosomal regions, 24,244,192 to 28,975,747 on chromosome 2 and 2,862,253 to 6,681,861 on chromosome 7 with high LOD scores (P > 0.05) are considered as the candidate loci. Candidate genes found located within these loci have no known functions or not likely to be related with regrowth. Twenty-five pairs of PCR primers were then designed on the basis of 13 SNPs and only 4 of them showed polymorphism between the parental alleles. One of the polymorphic SNP marker targeting the 27,773,017 bp on chromosome 2 showed good fitness of genotype to regrowth (P(χ2) = 0.195), yet the value is still low. More effort is needed to identify the candidate genes by SNP markers.

Library of Congress Subject Headings

Corn -- Genetics.
Agricultural ecology.


Includes bibliographical references



Number of Pages



South Dakota State University


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