Application of Association Mapping to Understanding the Genetic Diversity of Plant Germplasm Resources

Table 1

Linkage disequilibrium and association mapping studies in plants.

Species	Mating system	LD extent	Mapped traits	^*Approach used
Arabidopsis	Selfing	10–250 kb and 50–100 cM [20, 21, 64, 66, 67]	Flowering time, growth response, pathogen resistance, and branching architecture [66, 129, 145–148]	One way ANOVA, simple regression, SA, MLM
Maize	Outcrossing	200–2000 bp [43, 68], 3–500 kb [43, 69–71], 4–41 cM [9, 22]	Plant height, flowering time, endosperm color, starch production, maysin and chlorogenic acid accumulation, cell wall digestibility, forage quality, and oleic acid level [43, 69, 71, 87, 88, 149–154]	GLM, SA, MLM, WGA
Rice (indica, japonica and rufipogon)	Selfing	5–500 kb [73, 75, 76] 50–225 cM [74], 20–30 cM [155]	Multiple agronomic traits such as plant height, heading date, flag leaf length and width, tiller number, steam diameter, panicle length, grain length and width, grain length/width ratio, grain thickness, 1000-grain weight, width and length of milled rice grains [58, 155, 156]	DA, MLM, mixed model with multiple QTL effect
Barley	Selfing	10–50 cM [16, 77], 98–500 kb [51], 300 bp [78]	Yield, yield stability, heading date, flowering time, plant height, rachilla length, resistance to mildew, and leaf rust were associated with many different types of molecular markers [17, 18, 157, 158]	Pearson correlation; regression, ANOVA
Tetraaploid wheat	Selfing	10 and 20 cM [50]	N/A	N/A
Hexaploid wheat	Selfing	<1–10 cM [52, 56, 72]	Kernel size and milling, a high molecular weight glutenin and blotch resistance [52, 56, 159]	GLM-Q, LMM
Potato	Selfing	0.3–1 cM [25, 60], 3 cM [160]	Resistance to wilt disease, bacterial blight, Phytophtora, and potato quality (tuber shape, flesh color, under water weight, maturity, and etc.)[59, 60, 138, 160]	Nonparametric Mann-Whitney U test, standard two sample t-test, GMM
Soybean	Selfing	10–50 cM [79, 80],	Seed protein content [80]	WGA
Sorghum	Outcrossing	50 cM [44]	N/A	N/A
Grape	Vegetative propagation	5–10 cM [53]	N/A	N/A
Sugarcane	Outcrossing/Vegetative propagation	10 cM [10]	N/A	N/A
Sugar beet	Outcrossing	3 cM [81]	N/A	N/A
Forage grasses (silage maize and ryegrass)	Outcrossing	200–2000 bp [87–91]	Cold tolerance, flowering time and forage quality, water-soluble carbohydrate content [87, 88, 161, 162]	Multiple linear regression; ANOVA
Forest trees (Norway spruce, Loblolly pine, poplar, European aspen, Douglas-fir)	Outcrossing	100–200 bp [86], ~500–2000 bp [83–85]	Early-wood microfibril angle trait, wood density and wood growth rate [141, 163]	ANOVA; combination of LD and QTL mapping

^* MLM: mixed linear model [133]; GLM: general linear model without population structure [71]; GLM-Q: general linear model using population structure matrix (Q) or the least square solution to the fixed effects GLM [56]; DA: discriminant analysis [156]; SA-structured association [47]; LMM: linear mixed model [52]; WGA: whole genome association [154, 164, 165]; GMM: general mixed model [59]; ANOVA: analysis of variance test; N/A—not available (search of known major online library database as of December 2007).