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Open AccessArticle

Genomics-Enabled Analysis of Puroindoline b2 Genes Identifies New Alleles in Wheat and Related Triticeae Species

by Xiaoyan Li 1,†, Yin Li 2,†, Xiaofen Yu 1,†, Fusheng Sun 1, Guangxiao Yang 1,* and Guangyuan He 1,*
1
The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
2
Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2020, 21(4), 1304; https://doi.org/10.3390/ijms21041304
Received: 17 January 2020 / Revised: 7 February 2020 / Accepted: 11 February 2020 / Published: 14 February 2020
(This article belongs to the Special Issue Plant Genomics 2019)
Kernel hardness is a key trait of wheat seeds, largely controlled by two tightly linked genes Puroindoline a and b (Pina and Pinb). Genes homologous to Pinb, namely Pinb2, have been studied. Whether these genes contribute to kernel hardness and other important seed traits remains inconclusive. Using the high-quality bread wheat reference genome, we show that PINB2 are encoded by three homoeologous loci Pinb2 not syntenic to the Hardness locus, with Pinb2-7A locus containing three tandem copies. PINB2 proteins have several features conserved for the Pin/Pinb2 phylogenetic cluster but lack a structural basis of significant impact on kernel hardness. Pinb2 are seed-specifically expressed with varied expression levels between the homoeologous copies and among wheat varieties. Using the high-quality genome information, we developed new Pinb2 allele specific markers and demonstrated their usefulness by 1) identifying new Pinb2 alleles in Triticeae species; and 2) performing an association analysis of Pinb2 with kernel hardness. The association result suggests that Pinb2 genes may have no substantial contribution to kernel hardness. Our results provide new insights into Pinb2 evolution and expression and the new allele-specific markers are useful to further explore Pinb2’s contribution to seed traits in wheat. View Full-Text
Keywords: wheat; wheat genome; kernel hardness; Puroindoline; Puroindoline b-2 variants; genotype-to-phenotype association; synteny; phylogenetic analysis wheat; wheat genome; kernel hardness; Puroindoline; Puroindoline b-2 variants; genotype-to-phenotype association; synteny; phylogenetic analysis
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Li, X.; Li, Y.; Yu, X.; Sun, F.; Yang, G.; He, G. Genomics-Enabled Analysis of Puroindoline b2 Genes Identifies New Alleles in Wheat and Related Triticeae Species. Int. J. Mol. Sci. 2020, 21, 1304.

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