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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (2): 332-342.doi: 10.3724/SP.J.1006.2023.22015

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Genetic analysis of photosensitivity divergence among hybrids derived from rice sterile line Xiangling 628S

CHEN Sai-Hua1(), PENG Sheng1, YOU Yi-Wen1, ZHANG Lu-Yao1, WANG Kai3, XUE Ming1,*(), YANG Yuan-Zhu3,*(), WAN Jian-Min2   

  1. 1Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, Jiangsu, China
    2State Key Laboratory for Crop Genetics and Germplasm Enhancement / Jiangsu Plant Gene Engineering Research Center / Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
    3Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs / Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding / Yuan Longping High-Tech Agriculture Co., Ltd., Changsha 410128, Hunan, China
  • Received:2022-03-12 Accepted:2022-05-05 Online:2022-05-13 Published:2022-05-13
  • Contact: XUE Ming,YANG Yuan-Zhu E-mail:chensaihua@yzu.edu.cn;007747@yzu.edu.cn;yangyuanzhu@lpht.com.cn
  • Supported by:
    Jiangsu Agricultural Science and Technology Innovation Fund “Development of Rice Germplasms with Heat-tolerance Based on qTT12(CX(21)3100);Science and Technology Innovation Program of Hunan Province(2021NK1001)

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Abstract:

Xiangling 628S is a high quality thermosensitive male sterile line of two-line hybrid rice, whose hybrids have high-quality rice and is suit for light-cultivation, large-scale, and mechanized planting, and 40 new hybrid rice varieties have been approved and widely used. However, its hybrids had strong photosensitivity when it crossed with a large majority of mid-late cultivars, and headed late or even not heading under long-day (LD) conditions, which limited its application in the Yangtze River area. To explore the genetic mechanism of photosensitivity divergence among different hybrids, several key photosensitive loci in Xiangling 628S and its restorer lines were analyzed by allelism tests combined with sequence analysis. The results showed that Xiangling 628S had recessive e1e1, Se-1eSe-1e and dominant Hd5kHd5k, E2E2, E3E3, and EF-1tEF-1t, showing weak photosensitivity. The photosensitivity divergence in different hybrids was closely correlated with E1 (Ghd7) locus in restorer lines, but not with Se-1 (Hd1) and Hd5 (DTH8). Finally, we developed two functional molecular markers for genetic identification of E1 and Se-1 loci in restorer lines, which would speed up the selection of weak/non-sensitive hybrids of Xiangling 628S. Our study provides important theoretical guidance and technical supports for the utilization of Xiangling 628S in breeding, as well as hybrid breeding with other sterile lines.

Key words: rice, sterile line, photosensitive, genes, molecular marker

Table 1

Genotypes of seven pairs of test lines adopted in this study"

待测位点
Locus		 测验系名称
Test line name		 基因型*
Genotype*		 测验系名称
Test line name		 基因型
Genotype
E1 EG0 e1e1e2e2e3e3Se-1nSe-1nEf-1Ef-1 EG1 E1E1e2e2e3e3Se-1nSe-1nEf-1Ef-1
E2 EG0 e1e1e2e2e3e3Se-1nSe-1nEf-1Ef-1 EG2 e1e1E2E2e3e3Se-1nSe-1nEf-1Ef-1
E3 EG0 e1e1e2e2e3e3Se-1nSe-1nEf-1Ef-1 EG3 e1e1e2e2E3E3Se-1nSe-1nEf-1Ef-1
Se-1 ER E1E1Se-1eSe-1eEf-1Ef-1 LR E1E1Se-1uSe-1uEf-1Ef-1
Hd1 Nip E1E1Se-1nSe-1nEf-1Ef-1Hd5Hd5 NIL (hd1) E1E1Se-1eSe-1eEf-1Ef-1Hd5Hd5
Hd5 Nip E1E1Se-1nSe-1nEf-1Ef-1Hd5Hd5 NIL (Hd5) E1E1Se-1nSe-1nEf-1Ef-1Hd5kHd5k
Ef-1 T65m e1e1Se-1eSe-1eef-1ef-1 T65Ebm e1e1Se-1eSe-1eEf-1Ef-1

Table 2

Primers used in this study"

类别
Primer type		 引物名称
Primer name		 正向序列
Forward sequence (5'-3')		 反向序列
Reverse sequence (5'-3')
用于鉴定Ghd7的缺失
For identification of Ghd7 deletion		 M1 GAGACCGATTAAGGTTGAA CTGTTGGTCGCAGTCTATG
M2 CCGCCGTCGTTGCCGAAGAA ATGGGACCAGCAGCCGGAGAAG
M3 ATGCAAATCACATCCCACA CTTCATTTCTGCTGCCTAT
M4 TTGTCCAAGCTCAAGCCTAC CGAGAAGCAAATCCGGTAC
M5 AATGGAGCCAGATTGTTCT CTTCTGTTCCGTTCACCTTT
M6 ACAGCAGGGTATTAAGGTA TAGGCAAAGAGCTATTTCG
用于基因的克隆与测序For gene cloning and sequencing Ghd7-exon1 CACAAGCATTTCACAACCCTA AGGCAGCAGAAATGAAGAGT
Ghd7-exon2 TTGCTTATGCGTACATCTGG AGTGGTATATACGCACTGTAATTA
Hd1-FLcDNA AGAGAGGACAAACACAATAGC TGTCTAGAACTACTCCCACTG
DTH8-FLcDNA GCTAGTGTTGTTAGCTTCAC TAAACAGCATCAGCATCAACA
用于分子标记
For molecuar markers		 E1D CACAAGCATTTCACAACCCTA AGTGGTATATACGCACTGTAATTA
SeI TGCAGGTGCACTCCGCGAA GAGTCCACCTCCTCGTCCTTG

Table 3

Some “Lingliangyou” early hybrids (approved) and strong photosensitive combinations"

杂交组合
Combinations		 恢复系
Restorer lines		 长江中下游早稻审定情况
Approved situation in Yangtze River		 感光性
Photosensitivity
陵两优32 Lingliangyou 32 HY032 国审稻2014004 State certified 2014004
湘审稻2012006 Hunan certified 2012006		 弱Weak
陵两优21 Lingliangyou 21 H421 湘审稻2010007 Hunan certified 2012007 弱Weak
陵两优211 Lingliangyou 211 H211 国审稻2010003 State certified 2010003 弱Weak
陵两优02 Lingliangyou 02 ZR02 无 No 弱Weak
陵两优1063 Lingliangyou 1063 华恢1063 Huahui 1063 赣审稻2013010 Jiangxi certified 2013010 弱Weak
陵两优564 Lingliangyou 564 华恢564 Huahui 564 湘审稻2009052 Hunan certified 2009052 弱Weak
陵两优472 Lingliangyou 472 蜀恢527 Shuhui 527 无 No 强Strong
陵两优711 Lingliangyou 711 恩恢58 Enhui 58 无 No 强Strong
陵两优838 Lingliangyou 838 辐恢838 Fuhui 838 无 No 强Strong
陵两优182 Lingliangyou 182 R182 无 No 强Strong
陵两优207 Lingliangyou 207 先恢207 Xianhui 207 无 No 强Strong
陵两优1377 Lingliangyou 1377 R1377 无 No 强Strong

Fig. 1

Photosensitivity of Xiangling 628S and the test results of allelism tests A: heading date (HD) of Xiangling 628S under natural long-day and short-day conditions. B-H: heading date of different test lines and their hybrids with Xiangling 628S. The abscissa represents different test lines (the same as test lines in Table 1) and their hybrids with Xiangling 628S, the vertical coordinate represents the days of heading date. S means Xiangling 628S, S/test line means F1 derived from Xiangling 628S crossed with each test line. ** indicates significant differences between each pair of test lines or each pair of F1 lines at P < 0.01."

Table 4

Heading date (HD) of test lines and their F1 hybrids crossed with Xiangling 628S"

测定位点
Tested locus		 测验系(杂交F1)
Test lines
(hybrid F1)		 抽穗期
Heading date
(mean±SD, d)		 延迟抽穗
Delayed heading
(d)		 P值
P-value		 测验系(湘陵628S)基因型*
Genotypes of test lines
(Xiangling 628S) *
E1 EG0 71.25±0.71 20.42±2.78 5.64E-12 e1e1
EG1 91.67±2.07 E1E1
S/EG0 83.63±1.69 32.50±3.05 3.35E-16 e1e1
S/EG1 116.13±1.36
E2 EG0 71.25±0.71 4.75±1.51 4.43E-10 e2e2
EG2 76.00±0.80 E2E2
S/EG0 83.63±1.69 -1.63±4.30 0.18 E2E2
S/EG2 82.00±2.61
E3 EG0 71.25±0.71 14.25±1.47 1.17E-17 e3e3
EG3 85.50±0.76 E3E3
S/EG0 83.63±1.41 -0.34±3.91 0.76 E3E3
S/EG3 83.29±2.50
Se-1 ER 80.25±1.28 22.45±2.62 9.51E-17 Se-1eSe-1e
LR 102.70±1.34 Se-1uSe-1u
S/ER 97.13±2.47 13.37±3.05 1.08E-06 Se-1eSe-1e or Se-1nSe-1n
S/LR 110.50±0.58
Hd1 NIL (hd1) 79.00±1.05 6.60±3.06 3.21E-08 Se-1eSe-1e
Nip 85.60±2.01 Se-1nSe-1n
S/NIL (hd1) 102.56±2.01 8.77±3.54 4.44E-05 Se-1eSe-1e
S/Nip 111.33±1.53
Hd5 Nip 85.60±2.01 11.00±3.08 9.73E-12 Hd5Hd5
NIL (Hd5) 96.60±1.07 Hd5kHd5k
S/Nip 111.33±1.53 0.67±3.81 0.67 Hd5kHd5k
S/NIL (Hd5) 112.00±2.28
Ef-1 T65Ebm 75.75±0.96 22.05±2.83 4.50E-11 Ef-1Ef-1
T65m 97.80±1.87 ef-1ef-1
S/T65Ebm 81.20±0.92 7.30±3.09 1.25E-08 Ef-1tEf-1t
S/T65m 88.50±2.17
结果Result Xiangling 628S 81.75±2.20 e1e1Se-1eSe-1eE2E2E3E3Hd5kHd5kEf-1Ef-1

Fig. 2

Ghd7 genotype tested in parents of different “Lingliangyou” hybrids A: the structural diagram of Ghd7 gene. The white box represents the untranslated region, the gray box represents the exon region (exon 1 is from 1 to 444 bp and exon 2 is from 2090 to 2419 bp), and the lines represent the upstream, downstream or intron regions. M1-M6 represents the positions of markers. B: the different haplotypes of Ghd7 gene. The reference sequence is Nipponbare. Each base varied among these materials was highlighted. Their locations corresponding to the reference genome and the resulting amino acid changes were indicated at the bottom. Restorer lines are the same as in Table 3. Shuhui 527, Enhui 58, Fuhui 838, R182, and Xianhui 207 belonged to Hap1, and R1377 belonged to Hap2. C: the electrophoresis detection results of M1-M6 products."

Fig. 3

Hd1 and DTH8 genotypes tested in parents of different “Lingliangyou” hybrids A: the structure and haplotype analysis of Hd1 gene; B: the structure and haplotype analysis of DTH8 gene. The white boxes represent the untranslated regions, the gray boxes represent the exon regions (Hd1 has two exons, exon 1 is 1-828 bp, exon 2 is 829-1188 bp; DTH8 has an 894 bp exon), and the broken line indicates the intron region. The numbers mean the positions corresponding to the Nipponbare cDNA. AA shows the changes in amino acids. Frame Shift means a frameshift caused by the insertions or deletions. The same or different sequences of HAP1-4 compared to Nipponbare are highlighted in blue or in orange. The parents within the strong photosensitive hybrids are highlighted in bold when the genotypes are classified into different haplotypes."

Fig. 4

Development and identification of functional molecular markers A: E1D marker can be used to identify the deletion at E1 (Ghd7) locus, M: DNA ladder; B: SeI marker can be used to identify the 36 bp insertion at the Se-1 (Hd1) locus. Zhu 1S is the sterile donor of Xiangling 628S and the restorer lines are the same as those given in Table 3."

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