Genetic Diversity and Association Analysis of Protein and Oil Content in Food-type Soybean

Ainong Shi, Pengyin Chen, Bo Zhang, and Anfu Hou

University of Arkansas

• Food-type soybean has generated tremendous public interests in various soyfoods

- Large seeds for tofu, soymilk, andedamame- Small seeds for natto and bean sprouts

Background

•Few have reported the genetic structure and diversity of food-type soybean.

• Seed protein and oil contents are two main quality traits in soybean breeding effort.

•Association analysis based on linkage disequilibrium (LD) has recently become an alternative approach to map QTL in plants.

• SSR markers have been widely used to analyze genetic diversity and detect QTLs through linkage mapping and association analysis in many crops including soybean.

Objective

• To analyze genetic diversity in 105 food-type soybeans using 65 SSRs

• To conduct association analysis of protein and oil content in soybean

• 105 food-type soybeans collected from Japan, South Korea, and 6 states of USA

• 65 SSRs located on 20 soybean MLGs used for genotying in the 105 soybeans

• Allele diversity including allele number, allele frequency, gene diversity, and PIC value calculated by PowerMarker 3.25

• AMOVA implemented in Arlequin 3.11

• Genetic structure analyzed by Structure 2.2

• Association tests run with the mixed linear model method in TASSEL 2.0.1

Materials and Methods

Phenotypic and genotypic data

• Protein: 42.9% (36.96-50.0%) • Oil: 19.0% (13.8-22.5%) • r = -0.67 (protein-oil)

• Allele number: 10 (5-16)• Gene diversity: 0.82 (0.57-0.91) • PIC: 0.79 (0.42-0.89)

Results

• 105 food-type soybeans divided into three clusters (I, II and III), and further into six groups• Cluster I: S. Korea and Japan• Cluster II: USA lines• Cluster III: S. Korea

The genetic background in USA food-type lines were different from those lines from Japan and South Korea.

Genetic Diversity

• Cluster I: I-S and I-SJ• Cluster II: II-N, II-MK and II-IO

• Group I-S: 7 Southern Korea lines• Group I-SJ: 10 South Korea, 3 Japan, and 1 Missouri lines• Group II-N: 3 North Dakota, 2 South Korea, and 1 Virginia lines. • Group II-MK: 8 Missouri, 3 Kansas, and

1 Virginia lines• Group II-IO: 18 Iowa, 12 Ohio, 1 Missouri and 1 Virginia lines

• Cluster III: 26 South Korea, 2 Japan, and 2 Virginia. • Two lines, K32 (KS4302sp) and O105 (HF-AG5381) not clustered into any group

• 18 Iowa + 12 (out of 14) lines clustered into the group II-IO

• 3 (4) Kansas + 10 Missouri lines into II-MK

• 3 North Dakota lines into II-N

• 5 Virginia lines into III, II-MK, II-N, and II-IO.

• 5 Japanese lines into I-SJ and III

• 46 Korean lines into four groups:

8 to I-S, 10 to I-SJ, 2 to II-N, and 26 to III

AMOVA for geographic origin in the 105 soybeans

Source of variation d.f. Sum of squares

Variance components

Percentage variation

P value

Among Countries 2 237.84 0.380 0.99 < 0.001

Among states within USA

5

337.83 4.056 10.60 < 0.001

Within lines 97

3281.34

33.83 88.41 0.327

Total 104

3857.00 38.26

• The largest variance due to within soybean lines (88.41%)• Little variance due to among countries (less than 1%)• The variance among the six states of USA (10.60%) indicated genetic diversity existed among the states

Linkage disequlibrium (LD) value (R2, above diagonal line) and probability value (P, below diagonal line) for 65 markers in 105 soybean lines

LD parameter R2 was significant for most of the pairwise comparisons among 65 SSR markers.

SSR marker

LG Pos a

(cM)P R2 Marker/QTL reported in around the region

Marker Pos (cM) Reference

Satt300 A1 30.93 7.37E-05 0.191 A329_2 30.30 Mansur et al. (1996)

Satt187 A2 54.92 2.09E-06 0.456 Prot 17-4 48.5 – 49.5 SoyBase

Satt228 A2 154.11 6.85E-05 0.244 A505_1 132.30 Brummer et al. (1997)

Satt453 B1 123.96 7.06E-05 0.227 - - -

Satt577 B2 6.05 8.55E-04 0.093 A352_1 29.20 Lee et al. (1996)

Satt556 B2 73.21 4.49E-05 0.229 B142_1 43.60 Lee et al. (1996)

Satt281 C2 40.30 3.43E-07 0.424 - - -

Satt147 D1a 108.89 3.24E-04 0.237 Satt077 77.50 Csanadi et al. (2001)

Satt459 D1b 118.62 1.64E-06 0.303 Satt459 118.62 Hyten et al. (2004)

Satt268 E 44.25 1.56E-05 0.258 Satt268 44.27 Jun et al. (2007)

Satt146 F 1.92 2.44E-07 0.359 - - -

Satt586 F 3.63 6.42E-04 0.189 - - -

Satt352 G 50.53 4.61E-04 0.353 Satt564 57.32 Jun et al. (2007)

Satt571 I 18.50 1.01E-11 0.433 Satt571 18.50 Jun et al. (2007)

Satt496 36.40 Chung et al. (2003)

Satt523 L 27.92 3.42E-06 0.169 A023_1 36.70 Diers et al. (1992)

Satt229 L 93.89 3.54E-04 0.276 Satt006 92.00 Mansur et al. (1996)

Satt306 M 80.02 1.23E-04 0.143 Satt551 95.45 Jun et al. (2007)

Satt358 O 5.44 1.66E-04 0.233 Prot 21-5 4.44 – 6.44 SoyBase

Satt345 O 59.43 9.30E-05 0.337 Satt478 71.10 Speeht et al. (2001)19 putative QTLs for protein content (15 previously mapped using linkage analysis and 4 new identified)

SSR marker

LG Pos(cM)

P R2 Marker/QTL reported in around the region

Marker Pos (cM) Reference

Satt300 A1 30.93 1.53E-07 0.388 A329_2 30.30 Mansur et al. (1996)

Satt591 31.10 Hyten et al. (2003)

Satt187 A2 54.92 2.66E-04 0.194 T153_1A111_1

50.4267.33

Mansur et al. (1993)

Satt228 A2 154.11 7.78E-08 0.365 A505_1 132.30 Brummer et al. (1997)

Satt453 B1 123.96 9.73E-04 0.144 - - -

Satt577 B2 6.05 5.23E-07 0.275 A242_1 33.10 Diers et al. (1992)

Satt281 C2 40.30 1.15E-07 0.344 Satt432 38.00 Orf et al. (1999)

Satt147 D1a 108.89 4.92E-05 0.311 Satt147 108.89 Hyten et al. (2003)

Satt459 D1b 118.62 7.32E-05 0.169 Satt274 116.35 Panthee et al. (2005)

Satt146 F 1.92 1.94E-08 0.395 - - -

Satt114 F 63.69 8.17E-04 0.280 Satt510 71.40 Specht et al. (2001)

Satt571 I 18.50 9.95E-08 0.315 Satt571 18.50 Jun et al. (2007)

Satt239 36.94 Nichols et al. (2006)

Satt496 36.40 Chung et al. (2003)

Satt229 L 93.89 2.89E-08 0.435 Satt229 93.89 Hyten et al. (2003)

Satt358 O 5.44 6.62E-04 0.242 - - -

13 putative QTLs for oil content (10 previously mapped using linkage analysis and 3 new identified)

Summary

• 105 soybean lines were divided into three clusters and further clustered into six groups.

• A negative correlation was obtained between protein and oil contents (r = -0.67).

• 13 SSR markers distributed on 11 MLGs were identified to be significantly associated with oil content (p < 0.001 and R2% = 14.4 – 43.5).

• 19 SSR markers distributed on 14 MLGs were identified with protein content (P < 0.001, R2% = 14.3 – 45.6).

Thank you!