History of Champa rice
According to the History of Song Dynasty, there was a severe drought in Yangtze and Hui river valley areas and in the eastern and western Zhejiang paddy rice area in 1012 [4]. The emperor Zhenzong (a.d. 992–1022) heard that Champa rice was drought-resistant, early maturing, and non-photoperiod–sensitive [21]. He sent governors to Fujian Province and brought 30,000 bushels of Champa seeds and distributed them to farmers in the drought area. This Champa Kingdom was located in what is now central Vietnam. According to the history, as compared with Chinese rice, this Champa rice had longer panicles, no awn, less difference in grain size, could grow well in marginal land, and was drought-resistant and not sensitive to photoperiod [21, 22]. Therefore, Champa rice, with many good traits, came from Vietnam to Fujian (southern China) first and later to the Yangtze region (central China) during the early Song Dynasty in the 11th century. Barker explored the origin and spread of Champa rice and asked his colleague Susan McCouch at Cornell University about it. She mentioned she found a Champa rice in her collection and the DNA test indicated it was aus rice [5].
About 1000 rice landraces were brought from southern China to Taiwan by the Han people during late Ming to early Ching dynasty, around 400 years ago. They were propagated and maintained first by local farmers and then by rice breeders during the Japanese colonial time. All these accessions were indica and are now stored in the Germplasm Center, TARI. DGWG, one of the parental lines of IR8, was one of the accessions. These accessions were old landraces in China hundreds of years ago, but most, including DGWG, are not present in the current Chinese germplasm. We found 9 accessions that contained the term “Champa” in the TARI collection, as listed in the Materials section. Thus, many Champa rice accessions were used in the current study, including 3 from central Vietnam.
Most of the Champa rice genome has high heterozygosity
Rice is a selfing plant, and the genome of most modern varieties has high homozygosity. The homozygous and heterozygous SNPs of the Champa rice accessions used in the current study were calculated from the genome sequencing data, as indicated in the Methods section. Table 1 lists the 2 types of SNPs of Champa rice accessions and 2 modern varieties, Koshihikari and IR64, for comparison. The homozygous SNP numbers of all Champa accessions ranged from 2.1 to 2.5 million, as expected. However, the heterozygous SNPs, ranging from 0.6 to 1 M, were quite high in number as compared with the modern variety IR64: 445,517. Thus, similar to other landraces, the genome of Champa rice accessions still has high heterozygosity.
Table 1
Heterozygosity of Champa rice accessions.
Accessions
|
Homo SNPs
|
Hetero SNPs
|
Accessions
|
Homo SNPs
|
Hetero SNPs
|
Koshihikari
|
116,648
|
95,041
|
HsinChuLiuChan
|
2,259,093
|
683,763
|
IR64
|
2,120,758
|
446,517
|
LungYaChan
|
2,324,790
|
723,491
|
HeiChan
|
2,111,886
|
584,125
|
Rằn trắng
|
2,470,139
|
646,492
|
PaiJihTungChan
|
2,224,496
|
700,637
|
Nếp rẫy
|
2,442,619
|
588,552
|
PaiKoPuChan
|
2,247,859
|
707,499
|
Rằn đỏ
|
2,543,887
|
738,536
|
ChingKuoChan
|
2,207,227
|
696,877
|
Dee-Geo-Woo-Gen
|
2,476,224
|
1,087,516
|
WuChan
|
2,214,929
|
636,558
|
ChiayiWuKo
|
2,324,487
|
603,287
|
SNP, single nucleotide polymorphisms; homo, homozygous; hetero, heterozygous |
Some Champa rice accessions are resistant to biotic and abiotic stresses
The agronomic traits of about 3500 rice accessions in the TARI germplasm center were screened by rice breeders in the early 1960s [23]. All these accessions were grown in paddy fields for phenotyping. In addition to the yield components, flowering behavior, resistance to abiotic and biotic stresses etc. were also recorded. From the TARI monograph, Pai Ko Pu Chan, Wu Chan, Hsin Chu Liu Chan, and Lung Ya Chan are drought-resistant and Ching Kuo Chan, Wu Chan, Hsin Chu Liu Chan, Lung Ya Chan and DGWG are resistant to rice blast. According to the record of Vietnam Plant Resource Center, Rằn trắng is drought-resistant and Nếp rẫy is flooding-resistant. Thus, many of these Champa rice accessions are resistant to biotic and abiotic stresses.
Some Champa rice accessions are not sensitive to photoperiod and have the loss-of-function hd1 gene
Several recent reviews provided detailed information on the regulation of rice flowering (e.g., [24]; [25]; [26]). A few key genes have been suggested to affect flowering time, including Heading date 1 (Hd1), which encodes a B-box zinc-finger protein and is the ortholog of Arabidopsis CONSTANS (CO) [27]. The functional Hd1 protein is required for suppressing flowering under long-day conditions and promoting flowering under short-day conditions. Takahashi and Shimamoto [2] suggested that Hd1 was a possible target of selection to generate different flowering-time response in different regions. Using about 60 diverse rice accessions, Kim et al. [28] also concluded that accessions from tropical or sub-tropical regions preferentially have the non-functional alleles of hd1. In our previous analysis of data mining on the genome sequencing information in the public domain, we classified 10 loss-of-function haplotypes [29]. Rice plants with any of these 10 alleles did not respond to photoperiod and might have at least 2 growing seasons each year in sub-tropical and tropical regions. The whole-genome sequencing data for the Champa rice accessions from Vietnam and Taiwan revealed that several indeed had the loss-of-function hd1: DGWG, Hsin Chu Liu Chan, Wu Chien and Wu Chan contained type 7 hd1 and Lung Ya Chan type 13 hd1 (Table 2).
Table 2
Types of loss-of-function hd1 genes in the Champa rice accessions
Accession
|
Haplotype
|
Accession
|
Haplotype
|
Dee Geo Woo Gen
|
Type 7
|
Hei Chan
|
--
|
Taichung Native 1
|
Type 7
|
Pai Jih Tung Chan
|
--
|
Wu Chan
|
Type 7
|
Pai Ko Pu Chan
|
--
|
Hsin Chu Liu Chan
|
Type 7
|
Ching Kuo Chan
|
--
|
Taichung Woo Gen2
|
Type 7
|
Rằn trắng
|
--
|
Lung Ya Chan
|
Type 13
|
Nếp rẫy
|
--
|
|
|
Rằn đỏ
|
--
|
Also, according to the TARI monograph [23], DGWG, Pai Ko Pu Chan, Ching Kuo Chan, Wu Chan, Hsin Chu Liu Chan and Lung Ya Chan could grow twice a year in a paddy field and thus were not sensitive to photoperiod (i.e., they belonged to the early-flowering type).
Champa rice are indica instead of aus
To compare the relationship of Champa rice and other types, we used phylogenetic analysis of the Champa rice accessions along with some traditional accessions of japonica, indica and aus in Asia. A total of 52 accessions were used, and their types and collection locations are in Table S2. In total, 6 Aus, 5 japonica and 41 indica accessions, along with one wild rice, O. rufipogon, were used for analysis. All have > 10X sequencing redundancy. Those with the word Chan or Chien in the name from Taiwan (highlighted in green) were in the same clade as other Taiwan indica landraces (Fig. 1). Because DGWG, Woo Gen and the 7 newly sequenced Chan rice accessions clustered together, once again it was demonstrated that DGWG and Woo Gen were Champa rice. Together they were very close to the 3 accessions from central Vietnam (highlighted in blue). They were clustered with indica landraces collected from southeastern Asia but were quite far away from the aus accessions (highlighted in red). Thus, Champa rice was indica rather than aus. Together with absence of aus in the rice germplasm collection in China National Rice Research Institute [6], we suggest that Champa rice was indica type.
The impact of Champa rice
Many indica rice accessions were introduced to the Yangtze River region in China about 1000 years ago according to the History of Song Dynasty. Some points can be summarized: 1) Champa rice was already present in Southern China before the early Sung Dynasty, 2) many of the Champa rice accessions were resistant to biotic and abiotic stresses, and 3) perhaps there was no photoperiod-insensitive accession in Central China before Champa rice was introduced. Champa rice was cultivated in the Yangtze River area and southern China since then.
The sequence analysis and phenotype screening confirmed again that Champa rice accessions had several good agronomic traits: they were early ripening and thus could grow at least twice a year in subtropical and tropical regions and were resistant to biotic and abiotic stresses such as blast, drought and salt. Before the semi-dwarf varieties were available, the Champa rice accessions were very popular for rice production in Taiwan. In the early 20th century, many Champa rice landraces were subjected to pure line selection in Taiwan. Examples are Kaoshiung Ching Kuo Chan No. 1 and Kaoshiung Pai Ko Pu Chan [10]. After WWII, cross breeding was also used in the breeding program. The most famous variety was Taichung Native No. 1 (TN1), with the parental lines DGWG and Tsai Yuan Chon. This is the first semi-dwarf modern variety in the world and is lodging-resistant. TN1 was released at 1957 and very quickly became the leading variety in Taiwan. When the International Rice Research Institute (IRRI) was established at 1960, rice breeders brought DGWG to the IRRI and it was subjected to a breeding program. The famous miracle rice IR8 (DGWG x Pita) was released at 1966 and quickly became the hallmark rice variety for the “green revolution”. DGWG has been in the pedigree of at least 80% of the world’s modern indica rice varieties. Thus, Champa rice has played important roles in ancient and modern rice production.