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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (11): 1690-1702.doi: 10.3724/SP.J.1006.2020.02006


Effects of SSIIa and SSIIIa alleles and their interaction on eating and cooking quality under Wxmp background of rice

YAO Shu1(), ZHANG Ya-Dong1, LIU Yan-Qing1, ZHAO Chun-Fang1, ZHOU Li-Hui1, CHEN Tao1, ZHAO Qing-Yong1, ZHU Zhen1, Balakrishna Pillay2,*, WANG Cai-Lin1,*()   

  1. 1 Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Jiangsu High Quality Rice Research and Development Center / Nanjing Branch of China National Center for Rice Improvement, Nanjing 210014, Jiangsu, China
    2 School of Life Sciences, College of Agriculture, Engineering and Science at the University of KwaZulu-Natal (Westville Campus), Durban 4000, Natal, South Africa;
  • Received:2020-02-11 Accepted:2020-06-02 Online:2020-11-12 Published:2020-07-06
  • Contact: Pillay Balakrishna,Cai-Lin WANG E-mail:rice19820911@hotmail.com;clwang@jaas.ac.cn
  • Supported by:
    This study was supported by the Jiangsu Natural Science Foundation(BK20180302);the Jiangsu Agricultural Science and Technology Innovation Fund(CX[18]1001);the Jiangsu Key Research and Development Program(BE2018357);the Jiangsu Major New Varieties Creation Project(PZCZ201703);the Earmarked Fund of China Agriculture Research System(CARS-1-62);the Open Project of Key Laboratory of Jiangsu Crop Genomics and Molecular Breeding(PL201902)


In order to explain the variation of eating and cooking quality (ECQ) in different semi-waxy rice lines with Wxmp allele, sixty-four semi-waxy lines with Wxmp were developed by crossing from Wujing 13 and Kantou 194 (Milky Princess). The polymorphism of markers between the two parents was detected in soluble starch synthesis genes SSIIa and SSIIIa but not in other starch synthesis related genes. Genetic effects of SSIIa and SSIIIa on the amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and rapid visco analyzer (RVA) profile characteristics were analyzed in Wxmp rice lines. The results showed that SSIIa and SSIIIa had significant effects on the characteristic values of AC, GT, GC and RVA profile, and the interactive effects existed between the two genes. SSIIa2 and SSIIIa2 alleles (2 indicated that allele was derived from Wujing 13, the same as in the below) had a tendency to increase AC by 1.87% and 1.23%, respectively. This result was consistent in two years. There was no significant effect on GT for SSIIa and SSIIIa allelic variation, whereas the GT of SSIIa1SSIIIa1(1 indicated that the genes were derived from Kantou 194, the same as in the below) was significantly higher than that of SSIIa2SSIIIa2 by 1.34 °C. This indicated that GT was not significantly affected by single gene of SSIIa and SSIIIa but was remarkably influenced by the interaction of the two genes. The GC was significant varied among rice lines with different genotypes. The SSIIa2 and SSIIIa1 alleles could increase GC of 8.74 mm and 9.62 mm respectively. From the interaction of the two genes, the GC of SSIIa2SSIIIa1 genotype was 10.64 mm higher than the SSIIa1SSIIIa2 genotype, and was 16.95 mm higher than the SSIIa2SSIIIa2 genotype. The allele SSIIa2 increased the peak viscosity (PKV), hot paste viscosity (HPV), cool paste viscosity (CPV) and breakdown viscosity (BDV), but decreased the consistency viscosity (CSV) and setback viscosity (SBV). However, the effect of allele SSIIIa2 was just the opposite, which decreased the PKV, HPV, CPV, BDV and increased CSV and SBV. For the combination of SSIIa and SSIIIa, SSIIa2SSIIIa1 genotype showed the largest values in PKV, HPV and CPV, SSIIa2SSIIIa2genotype showed the largest values in BDV and CSV, and SSIIa2SSIIIa1 genotype showed the least value in SBV. These results provide a theoretical basis for improving eating and cooking quality of semi-waxy japonica rice.

Key words: semi-waxy japonica rice, SSIIa, SSIIIa, eating and cooking quality, allelic effects, interaction

Fig. 1

Development of 64 semi-waxy lines derived from Wujing 13/Kantou 194"

Table 1

Molecular markers of SSIIa, SSIIIa, and Wxmp genes"

Primer sequences (5′-3′)
Product size (bp)
Annealing temperature (℃)

Fig. 2

Detection of the Wxmp gene in 64 semi-waxy lines M: marker; 1-7: part of the semi-waxy lines; 8: Kantou 194; 9: Wujing 13."

Fig. 3

Detection of SSIIa (A) and SSIIIa (B) gene in 64 semi-waxy lines 1-7: part of the semi-waxy lines; 8: Kantou 194; 9: Wujing 13."

Table 2

The genotypes of SSIIa and SSIIIa locus for 64 semi-waxy lines derived from Wujing 13/Kantou 194"

Number of lines
Number of lines
SSIIa1 23 SSIIa1SSIIIa1 10
SSIIa2 41 SSIIa1SSIIIa2 13

Fig. 4

Frequency distribution of the AC, GC, and GT in 64 semi-waxy lines AC: amylose content; GC: gel consistency; GT: gelatinization temperature."

Fig. 5

Frequency distribution of the RVA profile characteristics in 64 semi-waxy lines PKV: peak viscosity; HPV: hot paste viscosity; CPV: cool paste viscosity; BDV: breakdown viscosity; SBV: setback viscosity; CSV: consistence viscosity."

Table 3

Analysis of variance on AC in different genotypes of SSIIa and SSIIIa locus and different years for 64 semi-waxy lines"

Source of variance
年内区组间Repetitions 4 0.26 0.07 0.72 NS
年份间Years 1 2.42 2.42 26.37 **
品系间Lines 63 268.90 4.27 46.51 **
11基因型内Within 11 genotype 9 32.10 3.57 38.87 **
12基因型内Within 12 genotype 12 11.91 0.99 10.82 **
21基因型内Within 21 genotype 38 66.85 1.76 19.17 **
22基因型内Within 22 genotype 1 37.65 37.65 410.30 **
基因型间Genotype 3 120.39 40.13 437.32 **
11+12与21+22间 Between 11+12 and 21+22 genotype 1 53.24 53.24 580.17 **
11与12间Between 11 and 12 genotype 1 0.03 0.03 0.30 NS
21与22间Between 21 and 22 genotype 1 67.12 67.12 731.48 **
年份×品系Years × lines 63 60.30 0.96 10.43 **
试验误差Error 252 23.12 0.09
总变异Total variation 383 355.01

Table 4

Allelic effect on AC of SSIIa and SSIIIa genes for 64 semi-waxy lines in 2013 and 2014"

AC in 2013
AC in 2014
Gene effect
SSIIa SSIIa1 9.05 8.85 8.95 1.87
SSIIa2 10.84 10.80 10.82
SSIIIa SSIIIa1 9.37 9.17 9.27 1.23
SSIIIa2 10.51 10.48 10.50

Table 5

Difference of AC for different genotypes in SSIIa and SSIIIa locus of 64 semi-waxy lines in 2013 and 2014"

2013 2014 两年平均
Mean of two years
Difference between
2013 and 2014
11 9.06 A 10.70 7.60 8.80 A 10.31 7.67 8.93 A 0.26
12 9.03 A 9.89 8.21 8.89 A 9.66 8.47 8.96 A 0.14
21 9.68 B 11.54 8.08 9.53 B 10.75 7.32 9.61 B 0.15
22 11.99 C 13.96 10.02 12.07 C 13.64 10.49 12.03 C -0.08

Table 6

Difference of GC and GT for different genotypes in SSIIa and SSIIIa locus of 64 semi-waxy lines"

糊化温度Gelatinization temperature 胶稠度Gel consistency
Mean (℃)
CV (%)
Mean (mm)
CV (%)
SSIIa1 70.59 1.26 1.78 73.78** 13.41 18.18
SSIIa2 70.36 1.01 1.44 82.53 10.28 12.46
SSIIIa1 70.49 1.11 1.57 81.47** 11.76 14.43
SSIIIa2 70.28 1.11 1.58 71.86 10.89 15.15
SSIIa1SSIIIa1 70.94 a 1.38 1.95 75.71 ab 16.29 21.52
SSIIa1SSIIIa2 70.33 ab 1.34 1.91 72.31 b 11.20 15.49
SSIIa2SSIIIa1 70.37 ab 1.02 1.45 82.95 a 10.05 12.12
SSIIa2SSIIIa2 69.60 b 1.21 1.89 66.00 b 10.12 15.21

Table 7

Difference of RVA profiles for different genotypes on SSIIa and SSIIIa locus of 64 semi-waxy lines"

SSIIa1 2495.0** 1438.0** 2104.8* 1056.9** 666.7* -390.2**
SSIIa2 2939.4 1651.1 2285.4 1288.3 634.3 -654.0
SSIIIa1 2828.4* 1589.7 2227.5 1238.8* 637.8* -600.9**
SSIIIa2 2597.6 1516.1 2191.4 1081.4 675.3 -406.1
SSIIa1SSIIIa1 2383.5 C 1333.2 B 1996.5 b 1050.3 B 663.3 B -387.0 a
SSIIa1SSIIIa2 2580.7 BC 1518.8 AB 2188.2 ab 1062.0 B 669.4 B -392.6 a
SSIIa2SSIIIa1 2942.5 A 1655.4 A 2286.7 a 1287.1 A 631.3 B -655.8 b
SSIIa2SSIIIa2 2816.0 AB 1482.0 AB 2234.0 ab 1334.0 A 752.0 A -582.0 b

Fig. 6

Interaction of different genotypes of SSIIa and SSIIIa locus AC: amylose content."

Table 8

Genetic effect of SSIIa and SSIIIa in different background of parents"

Background of parents
AC GT GC 最高黏度
崩解值BDV 回复值
SSIIa背景下SSIIIa的效应 Effect of SSIIIa under SSIIa background
Kantou 194
0.03 -0.61 -3.40* 197.20* 185.60* 191.70* 11.70 6.10 -5.60
Wujing 13
2.42* -0.77 -16.95 -126.50 -173.40 -52.70 46.90* 120.70* 73.80*
1.23 -0.69 -10.18 35.35 6.10 69.50 29.30 63.40 34.10
SSIIIa背景下SSIIa的效应 Effect of SSIIa under SSIIIa background
Kantou 194
0.67 -0.57 7.24* 559.00* 322.20* 290.20* 236.80 -32.00 -268.80
Wujing 13
3.07* -0.73 -6.31 235.30 -36.80 45.80 272.00* 82.60* -189.40*
1.87 -0.65 0.47 397.15 142.70 168.00 254.40 25.30 -229.10

Fig. 7

Appearance of semi-waxy rice with different AC"

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