Genetic Diversification of Starch Branching Enzymes during Maize Domestication and Improvement

Qi Li; Tiantian Yang; Wenye Rui; Houmiao Wang; Yunyun Wang; Zefeng Yang; Chenwu Xu; Pengcheng Li

doi:10.3390/genes14051068

Genetic Diversification of Starch Branching Enzymes during Maize Domestication and Improvement

Genes (Basel). 2023 May 11;14(5):1068. doi: 10.3390/genes14051068.

Authors

Qi Li¹, Tiantian Yang¹, Wenye Rui¹, Houmiao Wang^{1

2}, Yunyun Wang¹, Zefeng Yang^{1

2

3}, Chenwu Xu^{1

2

3}, Pengcheng Li^{1

2}

Affiliations

¹ Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China.
² Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
³ Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.

Abstract

Elucidating the genetic basis of starch pasting and gelatinization properties is crucial for enhancing the quality of maize and its utility as feed and industrial raw material. In maize, ZmSBE genes encode important starch branching enzymes in the starch biosynthesis pathway. In this study, we re-sequenced the genomic sequences of ZmSBEI, ZmSBEIIa, ZmSBEIIb, and ZmSBEIII in three lines called 335 inbred lines, 68 landrace lines, and 32 teosinte lines. Analyses of nucleotide polymorphisms and haplotype diversity revealed differences in the selection patterns of ZmSBEI, ZmSBEIIa, ZmSBEIIb, and ZmSBEIII during maize domestication and improvement. A marker-trait association analysis of inbred lines detected 22 significant loci, including 18 SNPs and 4 indels significantly associated with three maize starch physicochemical properties. The allele frequencies of two variants (SNP17249C and SNP5055G) were examined in three lines. The frequency of SNP17249C in ZmSBEIIb was highest in teosinte lines, followed by landrace lines, and inbred lines, whereas there were no significant differences in the frequency of SNP5055G in ZmSBEIII among the three lines. These results suggest that ZmSBE genes play an important role in the phenotypic variations in the starch physicochemical properties in maize. The genetic variants detected in this study may be used to develop functional markers for improving maize starch quality.

Keywords: association analysis; linkage disequilibrium; maize; starch branching enzyme; starch pasting and gelatinization properties.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

1,4-alpha-Glucan Branching Enzyme* / genetics
1,4-alpha-Glucan Branching Enzyme* / metabolism
Domestication
Polymorphism, Single Nucleotide / genetics
Starch
Zea mays* / genetics
Zea mays* / metabolism

Substances

1,4-alpha-Glucan Branching Enzyme
Starch

Grants and funding

This work was supported by the National Natural Science Foundation of China (31972487, 31902101, 32172009, and 32061143030), the National Key Research and Development Program of China (2022YFD1201804), the Jiangsu Province University Basic Science Research Project (21KJA210002), the Innovative Research Team of Universities in Jiangsu Province (none), the High-end Talent Project of Yangzhou University, and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Qing Lan Project of Jiangsu Province.