Transcription of Rice Green Revolution Gene sd1 is Clarified by Comparative RNA Diagnosis Using the Isogenic Background  

Motonori Tomita1 , Shota Matsumoto2
1. Molecular Genetics Laboratory, Faculty of Agriculture, Tottori University, 101, Minami 4-chome, Koyama-cho, Tottori 680-8553, Japan
2. Molecular Genetics Laboratory, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
Author    Correspondence author
Genomics and Applied Biology, 2011, Vol. 2, No. 5   doi: 10.5376/gab.2011.02.0005
Received: 14 Nov., 2011    Accepted: 29 Nov., 2011    Published: 20 Dec., 2011
© 2011 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Tomita and Matsumoto, 2011, Transcription of Rice Green Revolution Gene sd1 is Clarified by Comparative RNA Diagnosis Using the Isogenic Background,  Genomics and Applied Biology , 2011, Vol. 2, No.5 (DOI: 10.5376/gab.2011.02.0005)

Abstract

The sd1 allele, on the long arm of chromosome 1, encoding a defective C20-oxidase in the gibberellin (GA) biosynthesis pathway(GA 20-oxidase, OsGA20ox2) confers the semidwarf phenotype thatcontributed to Green Revolution in rice. It has yet to be known whether sd1 is transcribed. The two alleles at the sd1/OsGA20ox2 locus of each line, the Japanese leading varieties Koshihikari and Hikarishinseiki having inherited over 99.8% of the Koshihikari genome, except for sd1, were successfully distinguished by RT-PCR amplification of the first exon followed by digestion with PmaCI. RNA extracted from the leaves and roots was employed as the template then the 779 bp fragment was clearly cleaved into the 613 bp and 166 bp fragments by PmaCI digestion in Hikarishinseiki, but not cleaved in Koshihkari. Therefore, the RNA diagnosis figured out clarified that sd1 gene derived from Jukkoku was transcribed in Hikarishinseiki. It would be a first evidence of the transcription of sd1. Moreover, the taste and quality of Hikarishinseiki were in line with that of Koshihikari across Japan during two years, and it might be practically valuable as a brand rice description in the rice-producing districts of 13 prefectures in Japan.

Keywords
Rice (Oryza sativa L); Semidwarf ; Green Revolution; sd1; Transcription; RNA diagnosis; Trait performance; Lodging resistance

The development of high-yielding semidwarf varieties of wheat and rice led to a rapid increase in the global production of cereal grains, which more than doubled from 1960 to 1990 (Khush, 1999). The semidwarf rice variety, IR8, was developed by using the Chinese landrace ‘Dee-geo-woo-gen’ (DGWG) and released by the International Rice Research Institute (IRRI). It was known as “miracle rice” that responds well to fertilizer and produces an increased yield without culm elongation. Widespread adoption of the miracle rice  brought about a global “green revolution”, particularly in the monsoonal regions of Asia, where typhoons frequently occur during the harvesting season (Athwal, 1971; Khush, 1999).

The semidwarf character is one of a very important agronomic trait in crop breeding. In other countries, many other short-culm cultivars were developed using an independent source of semidwarfism germplasms, such as the Japanese indigenous landrace ‘Jukkoku’ (Okada et al., 1967), or γ-ray-induced semidwarf cultivars such as ‘Reimei’ in Japan and ‘Calrose 76’ in the USA (Foster and Rutger, 1978). Although dwarf varieties of rice have contributed to the dramatic improvement  and stabilization of yields worldwide, the dwarf stature of varieties derived from native or mutant maternal lines happens to be controlled by a single dwarf gene, sd1 (Kikuchi and Futsuhara, 1997; Monna et al., 2002; Spielmeyer et al., 2002; Sasaki et al., 2002; Ashikari et al., 2002). The sd1 allele is  located on the long arm of chromosome 1 (Cho et al., 1994a; 1994b; Maeda et al., 1997), which confers the semidwarf phenotype without  detrimental effects on grain yield (Hedden, 2003a; 2003b).

In Japan, Koshihikari suffers considerable lodging damage as a result of frequent powerful typhoons, and thus, developing of lodging-resistant cultivar has been a longstanding challenge. The author developed a dwarf Koshihikari-type cultivar, ‘Hikarishinseiki’ (Tomita, 2009; rice cultivar No.12273, Ministry of Agriculture, Forestry and Fisheries of Japan) using a dwarf cultivar line with the heading time same as Koshihikari-type, which was selected by intercrossing the F4 of Kanto No. 79 (early-heading mutant line derived from Koshihikari) and Jukkoku (a cultivar with a semi-dwarf gene, sd1), as the maternal parent, and backcrossed it with Koshihikari 8 times. Having over 99.8% background of the Koshihikari genome, except for sd1, Hikarishinseiki would be the first cultivar to be registered as a Koshihikari-type dwarf with sd1 in Japan (Tomita, 2009).

The dwarf feature of Hikarishinseiki is derived from the semidwarf gene sd1. sd1 is a defective gene of GA20ox-2, which encodes a defective C20-oxidase in the gibberellin (GA) biosynthesis pathway (GA 20-oxidase, OsGA20ox2) (Monna et al., 2002; Spielmeyer et al., 2002; Sasaki et al., 2002; Ashikari et al., 2002). However, it has yet to be known whether the sd1 gene possessed by Hikarishinseiki is transcribed. Subsequently, expression analysis was conducted by employing the RT-PCR method and PmaCI restriction enzyme digestion in order to clarify whether or not the sd1 gene carried by Hikarishinseiki is transcribed.

An increasing number of private agricultural producers across Japan have spontaneously started to grow Hikarishinseiki as a typhoon-resistant, easy-to-grow cultivar instead of Koshihikari. As the recommended cultivars become widespread, there will become a growing need for information that rewards producers for their efforts. Here, we analyzed the results of 24 performance tests aimed at determining recommended cultivars, carried out over a period of two years from 2006 to 2007.

1 Results
1.1 Transcription of sd1, defective allele of GA20ox-2
We performed expression analysis of the sd1 gene, which is introduced in the dwarf Koshihikari-type paddy rice variety ‘Hikarishinseiki’. The two alleles at the sd1/OsGA20ox2 locus on chromosome 1 of each line, Koshihikari and Hikarishinseiki, were distinguished by RT-PCR amplification of the first exon followed by digestion with PmaCI (Figure 1; Figure 2). A 779 bp fragment, employing one type of upper primer (F1) designed from the 1st exon and one type of downstream primer (R4) designed from the range of the 2nd to 3rd exon, contained only the exon. Moreover, 1,316 bp, 1,304 bp, 1,400 bp, and 1,366 bp fragments employing the four upper primers (F1~F4) designed from the 1st exon and the downstream primer (R6) designed from the 3rd exon, contained the 2nd intron. Lastly, 1,428 bp, 1,416 bp, and 1,478 bp fragments, obtained using three upstream primers (F1~F3) designed from the 1st exon and the RT primer (R5), contained both the 1st intron and 2nd intron. The target fragment was detected in these eight combinations of primers.


Figure 1 PCR primers designed for amplification of  cDNA derived from sd1 (GA20ox-2) transcript


Figure 2 PCR amplification of cDNA from sd1 (GA20ox-2) transcript and their PmaCI-digestion 


RNA extracted from the root was used as the template then the 779 bp fragment by primers F1 and R4 was cleaved into the 613 bp and 166 bp fragments by PmaCI digestion in Hikarishinseiki (Figure 2). Accordingly, it can be said that sd1 was transcribed in Hikarishinseiki.

1.2 Trait expression of sd1 in the isogenic background through multiregional tests
We analyzed the data of performance tests conducted in 17 regions across Japan over a period of two years from 2006 to 2007 (Table 1; Table 2).


Table 1 Comparison of agronomic characters of Koshihikari and Hikarishinseiki in 2006


Table 2 Comparison of agronomic characters of Koshihikari and Hikarishinseiki in 2007


Heading: During the 2-year study period, Hikarishinseiki headed 'extremely early', on average 0.25 days earlier than Koshihikari.

Plant height: The average height of Hikarishinseiki is 72.2 cm (77% of Koshihikari, range 74% ~ 81%), which is on average 20.6 cm (23%) shorter than Koshihikari. There was very little difference in the national average values for plant height and other characteristics during the 3–year study period, and as a result, shown values represent 3-year averages.

Degrees of lodging: The average degree of lodging was 0.2, which is between ± 0 ~ +3.8, indicating a significant improvement in lodging resistance.

Ear length: Ear length was 18.3 cm (98% that of Koshihikari), and the ratio to Koshihikari ear length ranged from 90% to 107%.

Number of ears: The average number of ears was 429/m2 (109% that of Koshihikari), and the ratio to Koshihikari ear number ranged from 96% to 117%. In Ishikawa prefecture, the number of ears was 10% more than that of Koshihikari in 2 consecutive years, and numbers were higher than Koshihikari in 90% of prefectures. Having a large number of ears is one of the notable characteristics of Hikarishinseiki.

Brown rice yield: The average brown rice yield over the 2 years was 56.5 kg/a (101% that from Koshihikari), but the ratio to that from Koshihikari varied significantly between regions from 86% to 124%. In some regions, average brown rice yield was ≥7% than that of Koshihikari in 2 consecutive years (Nagano: +13% in 2006, +8% in 2007, Ishikawa: +7% in 2006, +24% in 2007, Tottori: +8% in 2005, + 9% in 2006), while in other areas (Toyama and Tokushima) they were ≤5%, indicating regional differences in yield. Moreover, the yield and number of ears did not necessarily correspond. In some areas, Hikarishinseiki showed a larger yield but similar number of ears compared to Koshihikari.

Grain weight of brown rice: The average grain weight of Hikarishinseiki brown rice was 22.0 g (101% that of Koshihikari, ranging from 96% to 105%).

Brown rice quality: The average brown rice quality was 4.6 and the difference with that of Koshihikari ranged from +1.0 to -1.5. This score indicates ‘medium’ quality, the same class quality given to Koshihikari.

Taste: Overall taste was on average -0.1 using Koshihikari as the base cultivar. This score indicates a ‘better than average’ rating, equaling that of Koshihikari.

The difference between Hikarishinseiki and Koshihikari ranged from +0.25 to -0.64, and the average was -0.06 when Ishikawa prefecture (2005: -0.64, 2007: -0.59), where stricter taste standards are applied, was not included.

As shown above, although the characteristics of Hikarishinseiki as a dwarf variety of Koshihikari have now been clarified, significant regional differences in yield were revealed compared to Koshihikari. This may give us clues as to how yield can be further increased.

2 Discussion
Although Koshihikari is a dominant   variety of rice, representing 40% of the rice cropping area in Japan, problem arises as a result of lodging during heavy rainstorms. In order to solve this problem, the dwarf Koshihikari-type paddy rice variety ‘Hikarishinseiki’, which shows stronger lodging resistance than that of Koshihikari and has 99.8% or more of the Koshihikari genome, was developed.

‘Koshihikari sd1’ was developed from first crossing ‘Jukkoku’ (sd1sd1) with ‘Kanto No. 79’ (Sd1Sd1), an early-maturing mutant of ‘Koshihikari’ (Tomita, 2009). The pedigree method  was conducted in breeding program during the later generations of ‘Kanto 79’ x ‘Jikkoku’, and then the dwarf sd1 homozygous line  (‘Jikkoku’-type ‘Koshihikari’) whose heading date was the same as ‘Koshihikari’,  was selected and fixed in the F4 generation. The flanking substituted region adjacent to sd1 had been restricted by eight  recurrent backcrossing  between the Sd1sd1 descendants of ‘Jikkoku’-type ‘Koshihikari’ short line and ‘Koshihikari’ (Sd1Sd1) as the recurrent parent. The semidwarf phenotype (sd1sd1) was done by the BC8F3 generation, therefore in which ‘Koshihikari sd1’ line carried ≥99.8% of ‘Koshihikari’ background in their genome.

In this study, the two alleles at the sd1/OsGA20ox2 locus on chromosome 1 of each line, Koshihikari and Hikarishinseiki, were successfully distinguished by RT-PCR amplification of the first exon followed by digestion with PmaCI. RNA extracted from the root was employed as the template then the 779 bp fragment was clearly cleaved into the 613 bp and 166 bp fragments by PmaCI digestion in Hikarishinseiki, but not cleaved in Koshihkari. Therefore, it is concluded that sd1 gene derived from Jukkoku was transcribed in Hikarishinseiki. This study would be  a first evidence  of the transcription of sd1, a defective gene of GA20ox-2, that contributed to Green Revolution in rice.

Hikarishinseiki would be considered to be an alternative to  Koshihikari, being resistant to typhoon damage and easy to grow, and it was designated as a brand rice description in the rice-producing districts in Okayama, Tottori, Tokushima, Niigata, Kochi, Shiga, Mie, Kagawa, Hyogo, Kyoto, Hiroshima, Tochigi, and Kumamoto prefectures (by courtesy of Ministry of Agriculture, Forestry and Fisheries of Japan). In this study, the taste and quality of Hikarishinseiki were in line with Koshihikari across Japan during two years, and it would be  practically valuable from the standpoint of production and distribution. Nowadays, preliminary tests to determine recommended cultivars have been carried out extensively across Japan, with three prefectures, Tottori, Wakayama, and Kanagawa, having proceeded to main tests.

3 Methods
3.1 Transcription analysis of sd1
Expression analysis of sd1 was conducted by RT-PCR assay using RNA extracted from the leaves of Hikarishinseiki and Koshihikari grown since June 2009 at the farm of Tottori University and the roots of Hikarishinseiki and Koshihikari germinated on a Petri dish in the laboratory. After the reverse transcription reaction using an RT primer (R6:TCAGCTGGCCGCCTCGACCTGCGCCG) designed from the 3' end of sd1 (Os01g0883800), RT-PCR was performed with 24 combinations of the following types of primers: four upstream primers (F1:GGAGCCCAAGATCCCGGAGCCATTCGTG, F2: CGACCTGAGGATGGAGCCCAAGATCCCG, F3: GACTCCACCGCCGGCTCTGGCATTGC, F4: CACGCCACCACAGCCGCACCAACCAC designed from the 1st exon of sd1) and six downstream primers (R1: GAGGGTGCTGGAGAAGTAGTCGGCGAC designed from the 1st exon of sd1, R2: CACCCTCCCCATTGGCGCGAAGTCGG from the range of the 1st to 2nd exon, R3: TACCATGAAGGTGTCGCCGATGTTGATGACC from the 2nd exon, R4: CGTTCGACAGCGCCATGAAGGTGTCGCC from the range of the 2nd to 3rd exon, R5: TCAGCTGGCCGCCTCGACCTG from the 3rd exon, and R6 mentioned above designed from the 3' end). Primer designing was based on the public sequence of Nipponbare (http://rgp.dna.affrc.go.jp). Since sd1 confers GA20ox-2 and shares homology with GA20ox-1 (Os03g0856700), the primer was designed from the region showing low homology between GA20ox-2 and GA20ox-1, allowing distinct labeling of GA20ox-2 and GA20ox-1, respectively. PCR amplification took place in a 20 µL containing:  10 ng  genomic DNA, 1 µM of each primer, 0.4 mM dNTPs, 1 × GC buffer â… , 2.5 mM MgCl2, and 0.5 unit of LA Taq polymerase (TaKaRa) in a total volume of 20 µL. And using following cycling conditions: 35 cycles,  94°C 30 s,  58°C 30 s, and  72°C 1 min. PCR products were treated  with the restriction enzyme PmaCI (CAC↓GTG), which can detect a single base substitution site of sd1 in the 1st exon of sd1 from Hikarishinseiki according to Tomita (2009). The transcription product of sd1 was then analyzed.

3.2 Performance test of sd1 in the isogenic background
Performance tests were carried out in a paddy field at Tottori University, Koyama, during 2006 and 2007. ‘Hikarishinseiki’ and ‘Koshihikari’ were sown on 20 April 2006 and on 21 April 2007, and 128 seedlings per plot were transplanted with two replications on 15 and 17 May, respectively. Similar performance tests were conducted at experimental stations in Miyagi, Ibaraki, Kanagawa, Nagano, Mie, Toyama, Ishikawa Kyoto, Wakayama, Hyogo, Shimane, Okayama, Tokushima, Ehime, Oita and Kumamoto, which are spread across Japan.

The date was recorded as the heading date once when 50% of all panicles had emerged from the flag leaf sheath. Days-to-heading was the number of days from sowing date to heading date. Culm length, panicle length, number of panicles, leaf length, and leaf width were measured on 10 randomly selected individuals in each plot. Thousand-grain weight, grain yield of brown rice, grain quality, and eating quality were measured on bulks of 50 individuals. The means of traits were statistically compared using the t-test.

Author’s contributions
MT conceived and designed the study and wrote the manuscript. MT and SM performed the experiments and analyzed the data. Both of authors read and approved the final manuscript.

Acknowledgements
The authors would like to express our gratitude to Japan Science and Technology Agency (JST) for the Grant-in-Aid for Adaptable and Seamless Technology Transfer Program through Target-driven R & D (No. 08150094 and No. 08001167) that supported this work to Motonori Tomita. We thank to all those who provided test data from prefectures across Japan. 

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