Novel Sources of aus Rice for Zinc Deficiency Tolerance Identified Through Association Analysis Using High-Density SNP Array

doi:10.1016/j.rsci.2018.08.004

Abstract

Abstract:

Zinc (Zn) deficiency is a major soil constraint limiting rice crop growth and yield, yet the genetic control of tolerance mechanisms is still poorly understood. Here, we presented promising loci and candidate genes conferring tolerance to Zn deficiency and identified through association analysis using a 365 K single nucleotide polymorphism (SNP) marker array in a diverse aus (semi-wild type rice) panel. Tolerant accessions exhibited higher growth rate with relatively rare stress symptoms. Two loci on chromosomes 7 and 9 were strongly associated with plant vigor under Zn deficiency at a peak-stress stage. Based on previous microarray data from the same experimental plots, we highlighted four candidate genes whose expressions were accompanied by significant genotype and/or environment effects under Zn deficiency. Network-gene ontology supported known tolerance mechanisms, such as ascorbic acid pathway, and also suggested the importance of photosynthesis genes to overcome Zn deficiency symptoms.

Key words: aus, genome-wide association study, Zinc deficiency, rice

Lee Jae-Sung, Wissuwa Matthias, B. Zamora Oscar, M. Ismail Abdelbagi. Novel Sources of aus Rice for Zinc Deficiency Tolerance Identified Through Association Analysis Using High-Density SNP Array[J]. Rice Science, 2018, 25(5): 293-296.

Figures/Tables 2

References 16

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Locus ID	Chr	Position	Annotation		Expression ^a
LOC_Os07g45090	7	26 913 464-26 917 496	NADH-ubiquinone oxidoreductase		E (2.84 × 10^-2), G (5.94 × 10^-3)
LOC_Os07g45170	7	26 965 232-26 967 050	Protein phosphatase		E (1.13 × 10^-2)
LOC_Os09g26160	9	15 765 945-15 770 861	Glutamate receptor		E (2.58 × 10^-4), E × G (2.00 × 10^-2)
LOC_Os09g26190	9	15 790 768-15 800 951	CBS domain containing protein		E (2.10 × 10^-2), G (2.63 × 10^-2)
Locus ID	Network-ontology ^b			Significant marker position		P-value (R², %)	Allele
LOC_Os07g45090	Oxidation reduction; response to zinc ion and salt stress			na		na	na
LOC_Os07g45170	Response to oxidative and salt stresses; double-strand break repair			na		na	na
LOC_Os09g26160	Response to salt stress; ascorbic acid biosynthesis			15 770 497 (4th exon)		2.10 × 10^-5 (24)	A/G
LOC_Os09g26190	Photosynthesis; chlorophyll biosynthesis; protein to chloroplast thylakoid membrane			15 787 904 (3 kb upstream of 5′)		6.27 × 10^-6(28)	G/C

Locus ID	Chr	Position	Annotation		Expression ^a
LOC_Os07g45090	7	26 913 464-26 917 496	NADH-ubiquinone oxidoreductase		E (2.84 × 10^-2), G (5.94 × 10^-3)
LOC_Os07g45170	7	26 965 232-26 967 050	Protein phosphatase		E (1.13 × 10^-2)
LOC_Os09g26160	9	15 765 945-15 770 861	Glutamate receptor		E (2.58 × 10^-4), E × G (2.00 × 10^-2)
LOC_Os09g26190	9	15 790 768-15 800 951	CBS domain containing protein		E (2.10 × 10^-2), G (2.63 × 10^-2)
Locus ID	Network-ontology ^b			Significant marker position		P-value (R², %)	Allele
LOC_Os07g45090	Oxidation reduction; response to zinc ion and salt stress			na		na	na
LOC_Os07g45170	Response to oxidative and salt stresses; double-strand break repair			na		na	na
LOC_Os09g26160	Response to salt stress; ascorbic acid biosynthesis			15 770 497 (4th exon)		2.10 × 10^-5 (24)	A/G
LOC_Os09g26190	Photosynthesis; chlorophyll biosynthesis; protein to chloroplast thylakoid membrane			15 787 904 (3 kb upstream of 5′)		6.27 × 10^-6(28)	G/C

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