Genome-wide association study of pre-harvest sprouting resistance in Chinese wheat founder parents

Lin, Yu; Liu, Shihang; Liu, Yaxi; Liu, Yujiao; Chen, Guoyue; Xu, Jie; Deng, Mei; Jiang, Qiantao; Wei, Yuming; Lu, Yanli; Zheng, Youliang

doi:10.1590/1678-4685-GMB-2016-0207

Acessibilidade / Reportar erro

Brasil

Genetics and Molecular Biology

Español English

Brasil

Español English

sumário « anterior atual seguinte »

Sumário

Plant Genetics • Genet. Mol. Biol. 40 (3) • Jul-Sep 2017 • https://doi.org/10.1590/1678-4685-GMB-2016-0207 copy

Genome-wide association study of pre-harvest sprouting resistance in Chinese wheat founder parents

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Pre-harvest sprouting (PHS) is a major abiotic factor affecting grain weight and quality, and is caused by an early break in seed dormancy. Association mapping (AM) is used to detect correlations between phenotypes and genotypes based on linkage disequilibrium (LD) in wheat breeding programs. We evaluated seed dormancy in 80 Chinese wheat founder parents in five environments and performed a genome-wide association study using 6,057 markers, including 93 simple sequence repeat (SSR), 1,472 diversity array technology (DArT), and 4,492 single nucleotide polymorphism (SNP) markers. The general linear model (GLM) and the mixed linear model (MLM) were used in this study, and two significant markers (tPt-7980 and wPt-6457) were identified. Both markers were located on Chromosome 1B, with wPt-6457 having been identified in a previously reported chromosomal position. The significantly associated loci contain essential information for cloning genes related to resistance to PHS and can be used in wheat breeding programs.

Keywords:
General linear model; linkage disequilibrium; marker-trait associations; mixed linear model; seed dormancy

Variable	DF	Sum of squares	Mean square	F-value
Environments	4	31.19	7.80	892.13^* ***** Significant at p < 0.001.
Replications	5	1.65	0.33	37.72^* ***** Significant at p < 0.001.
Genotypes	79	22.69	0.29	32.86^* ***** Significant at p < 0.001.
G × E	316	18.09	0.06	6.72^* ***** Significant at p < 0.001.

Environment	Mean	SD	Min	Max	CV
12WJ	22.46%	0.23	0.00%	97.00%	103.74%
12YA	41.99%	0.28	0.00%	99.00%	67.76%
13WJ	90.86%	0.13	27.00%	100.00%	14.33%
13YA	82.68%	0.22	0.00%	100.00%	26.26%
14CZ	49.33%	0.31	1.00%	100.00%	63.82%

	PG-12WJ	PG-12YA	PG-13WJ	PG-13YA	PG-14CZ	Mean
PG-12YA	0.604^ significant at p < 0.01.
PG-13WJ	0.430^ significant at p < 0.01.	0.351^ significant at p < 0.01.
PG-13YA	0.167	0.344^ significant at p < 0.01.	0.305^ significant at p < 0.01.
PG-14CZ	0.654^ significant at p < 0.01.	0.680^ significant at p < 0.01.	0.556^ significant at p < 0.01.	0.436^ significant at p < 0.01.
Mean	0.766^ significant at p < 0.01.	0.839^ significant at p < 0.01.	0.630^ significant at p < 0.01.	0.581^ significant at p < 0.01.	0.903^ significant at p < 0.01.
BLUP	0.722^ significant at p < 0.01.	0.833^ significant at p < 0.01.	0.626^ significant at p < 0.01.	0.580^ significant at p < 0.01.	0.912^ significant at p < 0.01.	0.995^ significant at p < 0.01.

Environment^a a 13WJ, Wenjiang 2013; 13YA, Ya'an 2013.	Marker^b b significant at the threshhold of -log10(p) = 3.782.	Locus	Locus position (^c c the Chromosome and position of DArT markers were from the Triticarte consensus map 3.0 (http://www.triticarte.com.au/). M)	-Log₁₀^(p)	Marker R² (%)
13YA	wPt-668205	1A	473.36	3.92	21.19
13WJ	wPt-6457	1B	104.00	4.47	36.82
13WJ	tPt-7980	1B	365.57	5.34	29.94

Sociedade Brasileira de Genética Rua Cap. Adelmio Norberto da Silva, 736, 14025-670 Ribeirão Preto SP Brazil, Tel.: (55 16) 3911-4130 / Fax.: (55 16) 3621-3552 - Ribeirão Preto - SP - Brazil
E-mail: editor@gmb.org.br

Acompanhe os números deste periódico no seu leitor de RSS

[1] Send correspondence to Yaxi Liu. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, P.R. China. E-mail: liuyaxi@sicau.edu.cn

	PG-12WJ	PG-12YA	PG-13WJ	PG-13YA	PG-14CZ	Mean
PG-12YA	0.604^ significant at p < 0.01.
PG-13WJ	0.430^ significant at p < 0.01.	0.351^ significant at p < 0.01.
PG-13YA	0.167	0.344^ significant at p < 0.01.	0.305^ significant at p < 0.01.
PG-14CZ	0.654^ significant at p < 0.01.	0.680^ significant at p < 0.01.	0.556^ significant at p < 0.01.	0.436^ significant at p < 0.01.
Mean	0.766^ significant at p < 0.01.	0.839^ significant at p < 0.01.	0.630^ significant at p < 0.01.	0.581^ significant at p < 0.01.	0.903^ significant at p < 0.01.
BLUP	0.722^ significant at p < 0.01.	0.833^ significant at p < 0.01.	0.626^ significant at p < 0.01.	0.580^ significant at p < 0.01.	0.912^ significant at p < 0.01.	0.995^ significant at p < 0.01.