Genetic variation in the chloroplast genome suggests multiple domestication of cultivated Asian rice (Oryza sativa L.)

Complete chloroplast genome sequence of Camellia sinensis: genome structure, adaptive evolution, and phylogenetic relationships

The chloroplast (cp) genome holds immense potential for a variety of applications including species identification, phylogenetic analysis, and evolutionary studies. In this study, we utilized Illumina NovaSeq 6000 to sequence the DNA of Camellia sinensis L. cultivar 'Zhuyeqi', followed by the assembly of its chloroplast genome using SPAdes v3.10.1, with subsequent analysis of its features and phylogenetic placement. The results showed that the cp genome of 'Zhuyeqi' was 157,072 bp, with a large single-copy region (LSC, 86,628 bp), a small single-copy region (SSC,18,282 bp), and two inverted repeat regions (IR, 26,081 bp). The total AT and GC contents of the cp genome of 'Zhuyeqi' were observed to be 62.21% and 37.29%, respectively. The cp genome encoded 135 unique genes, including 90 protein-coding genes (CDS), 37 tRNA genes, and 8 rRNA genes. Moreover, 31 codons and 247 simple sequence repeats (SSRs) were identified. The cp genomes of 'Zhuyeqi' were found to be relatively conserved, with conservation observed in the IR region, which showed no evidence of inversions or rearrangements. The five regions with the largest variations were identified, with four regions (rps12, rps19, rps16, and rpl33) located in the LSC region and one divergent region (trnI-GAU) in the IR region. Phylogenetic analysis revealed that Camellia sinensis (KJ996106.1) was closely related to 'Zhuyeqi', indicating a close phylogenetic relationship between these two species. These findings could provide important genetic information for further research into breeding of tea tree, phylogeny, and evolution of Camellia sinensis.

Fine-scale genetic structure of the rice landrace population in Japan

Rice cultivation was introduced into Japan 3000 years ago and has expanded across the country and encompasses a wide variety of environmental conditions. Here, we elucidated the differentiation of the genetic population structure of 1037 rice landraces across Japan. Using 4451 polymorphisms derived from genome-wide analysis of double-digest restriction-site-associated DNA analysis, population genomics including ADMIXTURE and principal component analysis was carried out. These landraces were classified into nine subpopulations based on geographical origin. Massive-scale genotyping and diversity analysis demonstrated that the differentiation of genetic population structure in rice landraces across Japan might consist of two phases, namely western to eastern and southern to northern phases. The differentiation of genetic population structure was detected only in landraces from three geographical regions, Hokuriku, Tohoku, and Hokkaido, as the southern to northern phase. Conversely, differentiation was not observed in landraces from six geographical regions, Kyushu, Shikoku, Chugoku, Kinki, Tokai, and Kanto, as the western to eastern phase. The genetic population structure may have facilitated the expansion of genetic diversity among local regions.

A Journey to the West: The Ancient Dispersal of Rice Out of East Asia

Rice is one of the most culturally valued and widely grown crops in the world today, and extensive research over the past decade has clarified much of the narrative of its domestication and early spread across East and South Asia. However, the timing and routes of its dispersal into West Asia and Europe, through which rice eventually became an important ingredient in global cuisines, has remained less clear. In this article, we discuss the piecemeal, but growing, archaeobotanical data for rice in West Asia. We also integrate written sources, linguistic data, and ethnohistoric analogies, in order to better understand the adoption of rice outside its regions of origin. The human-mediated westward spread of rice proceeded gradually, while its social standing and culinary uses repeatedly changing over time and place. Rice was present in West Asia and Europe by the tail end of the first millennium BC, but did not become a significant crop in West Asia until the past few centuries. Complementary historical, linguistic, and archaeobotanical data illustrate two separate and roughly contemporaneous routes of westward dispersal, one along the South Asian coast and the other through Silk Road trade. By better understanding the adoption of this water-demanding crop in the arid regions of West Asia, we explore an important chapter in human adaptation and agricultural decision making.

Variant biochemical responses: intrinsic and adaptive system for ecologically different rice varieties

India has a diverse range of agro-ecological conditions which support the cultivation of different rice varieties differing in the adaptation which is so important for sustainable development of rice crop. Specific ecotypes of rice adapted to diverse conditions have divergence in their morphology, physiology, biochemistry, molecular function, agronomy, and stress response. In the present study, 12 different rice varieties viz., PB-1, PB-1509, Pusa-RH-10, CSR-30, HKR-47, PR-126, Govind, Sharbati, ADT-37, ADT-39, ADT-45, White Ponni, were selected for the study of intrinsic biochemical behaviour and these varieties belong to different Agro-ecological zones and basmati or non-basmati rice varieties. Amongst intrinsic biochemicals activity, the differential response of radical scavenging, superoxide dismutase (SOD), catalase (CAT) and guaiacol peroxidase (POX) activities, were observed in the selected rice varieties at 14 days old seedling stage, developed under controlled growth conditions. Comparatively, North India region rice varieties displayed an enhanced intrinsic biochemical response than south India region rice varieties. Similarly, basmati rice varieties showed increased biochemical response compared to non-basmati rice varieties. Thus, the differential biochemical responses (radical scavenging, SOD, CAT, and POX activities) observed creates a significant difference between rice varieties and provides valuable information about rice ecotype-biochemical interaction for sustainable adaptive value under different ecological conditions.

Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats

The course, tempo and mode of chloroplast genome evolution remain largely unknown, resulting in limited knowledge about how plant plastome gene and genome evolve during the process of recent plant speciation. Here, we report the complete plastomes of 22 closely related Oryza species in chronologically ordered stages and generate the first precise map of genomic structural variation, to our knowledge. The occurrence rapidity was estimated on average to be ~7 insertions and ~15 deletions per Myr. Relatively fewer deletions than insertions result in an increased repeat density that causes the observed growth of Oryza chloroplast genome sizes. Genome-wide scanning identified 14 positively selected genes that are relevant to photosynthesis system, eight of which were found independently in shade-tolerant or sun-loving rice species. psaA seemed positively selected in both shade-tolerant and sun-loving rice species. The results show that adaptive evolution of chloroplast genes makes rice species adapt to diverse ecological habitats related to sunlight preferences.

Origin of the Aromatic Group of Cultivated Rice (Oryza sativa L.) Traced to the Indian Subcontinent

The aromatic group of Asian cultivated rice is a distinct population with considerable genetic diversity on the Indian subcontinent and includes the popular Basmati types characterized by pleasant fragrance. Genetic and phenotypic associations with other cultivated groups are ambiguous, obscuring the origin of the aromatic population. From analysis of genome-wide diversity among over 1,000 wild and cultivated rice accessions, we show that aromatic rice originated in the Indian subcontinent from hybridization between a local wild population and examples of domesticated japonica that had spread to the region from their own center of origin in East Asia. Most present-day aromatic accessions have inherited their cytoplasm along with 29-47% of their nuclear genome from the local Indian rice. We infer that the admixture occurred 4,000-2,400 years ago, soon after japonica rice reached the region. We identify aus as the original crop of the Indian subcontinent, indica and japonica as later arrivals, and aromatic a specific product of local agriculture. These results prompt a reappraisal of our understanding of the emergence and development of rice agriculture in the Indian subcontinent.

Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice

Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.

Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing

BACKGROUND

Chloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic.

RESULTS

A total of 3677 variations across the chloroplast genome were identified with an average density of 27.33 per kb, in which wild rice showing a higher variation density than cultivated groups. Chloroplast genome nucleotide diversity investigation indicated a high degree of diversity in wild rice than in cultivated rice. Genetic distance estimation revealed that African rice showed a low level of breeding and connectivity with the Asian rice, suggesting the big distinction of them. Population structure and principal component analysis revealed the existence of clear clustering of African and Asian rice, as well as the indica and japonica in Asian cultivated rice. Phylogenetic analysis based on maximum likelihood and Bayesian inference methods and the population splits test suggested and supported the independent origins of indica and japonica within Asian cultivated rice. In addition, the African cultivated rice was thought to be domesticated differently from Asian cultivated rice.

CONCLUSIONS

The chloroplast genome variation architecture in Asian and African rice are different, as well as within Asian or African rice. Wild rice and cultivated rice also have distinct nucleotide diversity or genetic distance. In chloroplast level, the independent origins of indica and japonica within Asian cultivated rice were suggested and the African cultivated rice was thought to be domesticated differently from Asian cultivated rice. These results will provide more candidate evidence for the further rice chloroplast genomic and evolution studies.

Between China and South Asia: A Middle Asian corridor of crop dispersal and agricultural innovation in the Bronze Age

The period from the late third millennium BC to the start of the first millennium AD witnesses the first steps towards food globalization in which a significant number of important crops and animals, independently domesticated within China, India, Africa and West Asia, traversed Central Asia greatly increasing Eurasian agricultural diversity. This paper utilizes an archaeobotanical database (AsCAD), to explore evidence for these crop translocations along southern and northern routes of interaction between east and west. To begin, crop translocations from the Near East across India and Central Asia are examined for wheat (Triticum aestivum) and barley (Hordeum vulgare) from the eighth to the second millennia BC when they reach China. The case of pulses and flax (Linum usitatissimum) that only complete this journey in Han times (206 BC-AD 220), often never fully adopted, is also addressed. The discussion then turns to the Chinese millets, Panicum miliaceum and Setaria italica, peaches (Amygdalus persica) and apricots (Armeniaca vulgaris), tracing their movement from the fifth millennium to the second millennium BC when the Panicum miliaceum reaches Europe and Setaria italica Northern India, with peaches and apricots present in Kashmir and Swat. Finally, the translocation of japonica rice from China to India that gave rise to indica rice is considered, possibly dating to the second millennium BC. The routes these crops travelled include those to the north via the Inner Asia Mountain Corridor, across Middle Asia, where there is good evidence for wheat, barley and the Chinese millets. The case for japonica rice, apricots and peaches is less clear, and the northern route is contrasted with that through northeast India, Tibet and west China. Not all these journeys were synchronous, and this paper highlights the selective long-distance transport of crops as an alternative to demic-diffusion of farmers with a defined crop package.

Rice Varieties in Archaic East Asia: Reduction of Its Diversity from Past to Present Times

The Asian cultivated rice, Oryza sativa, is one of the most important crops feeding more than a third of global population. In spite of the studies for several decades, the origin and domestication history of rice varietal groups, japonica and indica, have not been fully unveiled. Genetic information of ancient rice remains is essential for direct and exclusive insight into the domestication history of rice. We performed ancient DNA analysis of 950- to 2,800-year-old rice remains excavated from Japan and Korea. We found the presence of both japonica- and indica-type varieties in the Yayoi period and the middle ages of Japan and the middle part of Korea Peninsula 2,000 years ago. It is popularly considered that japonica has been exclusively cultivated in northern part of East Asia including Japan and Korea. Our result disclosed unexpectedly wide diversity of rice varieties in archaic East Asia. The present results from ancient rice DNA reveal an exclusive insight for the domestication history of rice which is not provided as far as contemporary rice.

Genetic Relationship in Cicer Sp. Expose Evidence for Geneflow between the Cultigen and Its Wild Progenitor

There is a debate concerning mono- or poly-phyletic origins of the Near Eastern crops. In parallel, some authors claim that domestication was not possible within the natural range of the wild progenitors due to wild alleles flow into the nascent crops. Here we address both, the mono- or poly-phyletic origins and the domestications within or without the natural range of the progenitor, debates in order to understand the relationship between domesticated chickpea (Cicer arietinum L.) and its wild progenitor (C. reticulatum Ladizinsky) with special emphasis on its domestication centre in southeastern Turkey. A set of 103 chickpea cultivars and landraces from the major growing regions alongside wild accessions (C. reticulatum, C. echinospermum P.H Davis and C. bijugum K.H. Rech) sampled across the natural distribution range in eastern Turkey were genotyped with 194 SNPs markers. The genetic affinities between and within the studied taxa were assessed. The analysis suggests a mono-phyletic origin of the cultigen, with several wild accession as likely members of the wild stock of the cultigen. Clear separation between the wild and domesticated germplasm was apparent, with negligible level of admixture. A single C. reticulatum accession shows morphological and allelic signatures of admixture, a likely result of introgression. No evidence of geneflow from the wild into domesticated germplasm was found. The traditional farming systems of southeaster Turkey are characterized by occurrence of sympatric wild progenitor-domesticated forms of chickpea (and likewise cereals and other grain legumes). Therefore, both the authentic crop landraces and the wild populations native to the area are a unique genetic resource. Our results grant support to the notion of domestication within the natural distribution range of the wild progenitor, suggesting that the Neolithic domesticators were fully capable of selecting the desired phenotypes even when facing rare wild-domesticated introgression events.

The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng

Panax ginseng C.A. Meyer (P. ginseng) is an important medicinal plant and is often used in traditional Chinese medicine. With next generation sequencing (NGS) technology, we determined the complete chloroplast genome sequences for four Chinese P. ginseng strains, which are Damaya (DMY), Ermaya (EMY), Gaolishen (GLS), and Yeshanshen (YSS). The total chloroplast genome sequence length for DMY, EMY, and GLS was 156,354 bp, while that for YSS was 156,355 bp. Comparative genomic analysis of the chloroplast genome sequences indicate that gene content, GC content, and gene order in DMY are quite similar to its relative species, and nucleotide sequence diversity of inverted repeat region (IR) is lower than that of its counterparts, large single copy region (LSC) and small single copy region (SSC). A comparison among these four P. ginseng strains revealed that the chloroplast genome sequences of DMY, EMY, and GLS were identical and YSS had a 1-bp insertion at base 5472. To further study the heterogeneity in chloroplast genome during domestication, high-resolution reads were mapped to the genome sequences to investigate the differences at the minor allele level; 208 minor allele sites with minor allele frequencies (MAF) of ≥0.05 were identified. The polymorphism site numbers per kb of chloroplast genome sequence for DMY, EMY, GLS, and YSS were 0.74, 0.59, 0.97, and 1.23, respectively. All the minor allele sites located in LSC and IR regions, and the four strains showed the same variation types (substitution base or indel) at all identified polymorphism sites. Comparison results of heterogeneity in the chloroplast genome sequences showed that the minor allele sites on the chloroplast genome were undergoing purifying selection to adapt to changing environment during domestication process. A study of P. ginseng chloroplast genome with particular focus on minor allele sites would aid in investigating the dynamics on the chloroplast genomes and different P. ginseng strains typing.

Nuclear and chloroplast diversity and phenotypic distribution of rice (Oryza sativa L.) germplasm from the democratic people's republic of Korea (DPRK; North Korea)

BACKGROUND

Rice accounts for 43% of staple food production in the Democratic People's Republic of Korea (DPRK). The most widely planted rice varieties were developed from a limited number of ancestral lines that were repeatedly used as parents in breeding programs. However, detailed pedigrees are not publicly available and little is known about the genetic, phenotypic, and geographical variation of DPRK varieties.

RESULTS

We evaluated 80 O. sativa accessions from the DPRK, consisting of 67 improved varieties and 13 landraces. Based on nuclear SSR analysis, we divide the varieties into two genetic groups: Group 1 corresponds to the temperate japonica subpopulation and represents 78.75% of the accessions, while Group 2 shares recent ancestry with indica varieties. Interestingly, members of Group 1 are less diverse than Group 2 at the nuclear level, but are more diverse at the chloroplast level. All Group 2 varieties share a single Japonica maternal-haplotype, while Group 1 varieties trace maternal ancestry to both Japonica and Indica. Phenotypically, members of Group 1 have shorter grains than Group 2, and varieties from breeding programs have thicker and wider grains than landraces. Improved varieties in Group 1 also show similar and/or better levels of cold tolerance for most traits, except for spikelet number per panicle. Finally, geographic analysis demonstrates that the majority of genetic variation is located within regions that have the most intensive rice cultivation, including the Western territories near the capital city Pyungyang. This is consistent with the conscious and highly centralized role of human selection in determining local dispersion patterns of rice in the DPRK.

CONCLUSIONS

Diversity studies of DPRK rice germplasm revealed two genetic groups. The most widely planted group has a narrow genetic base and would benefit from the introduction of new genetic variation from cold tolerant landraces, wild accessions, and/or cultivated gene pools to enhance yield potential and performance.

Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum

Heading date is one of the most important quantitative traits responsible for the domestication of rice. We compared a 155-kb reference segment of the Oryza sativa ssp. japonica cv. Nipponbare genome surrounding Hd1, a major heading date gene in rice, with orthologous regions from nine diploid Oryza species that diverged over a relatively short time frame (∼16 My) to study sequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare and contrast the evolution in a more distant relative of rice. Consistent with other observations at the adh1/adh2, monoculm1, and sh2/a1 loci in grass species, we found high gene colinearity in the Hd1 region amidst size differences that were lineage specific and long terminal repeat retrotransposon driven. Unexpectedly, the Hd1 gene was deleted in O. glaberrima, whereas the O. rufipogon and O. punctata copies had degenerative mutations, suggesting that other heading date loci might compensate for the loss or nonfunctionality of Hd1 in these species. Compared with the japonica Hd1 region, the orthologous region in sorghum exhibited micro-rearrangements including gene translocations, seven additional genes, and a gene triplication and truncation event predating the divergence from Oryza.

Genetic diversity and evolutionary relationships in genus Oryza revealed by using highly variable regions of chloroplast DNA

We studied the phylogeny of the genus Oryza using chloroplast DNA sequences. To identify regions containing sufficient variation for elucidating the relationship of closely related species with fine resolution and high reliability, we first compared the complete chloroplast sequences of Oryza sativa japonica, O. sativa indica, and O. nivara, and identified regions containing many variant sites. Nucleotide sequences of the variant regions were newly determined in 19 Oryza species including 58 cultivated and wild strains. An in silico pre-analysis of the whole chloroplast genome and subsequent nucleotide sequencing of the regions with the greatest number of variant sites, which were disclosed to be hot spots by the in silico pre-analysis, enabled us to examine genetic diversity in the genus Oryza with excellent resolution. Based on phylogenetic trees constructed using highly diverged regions in the chloroplast genome, we discuss the maternal relationships among Oryza species.

Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus

Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element in the lineages. In that aim, we used a combination of Southern hybridization with a reverse transcriptase (RT) probe and an adapter-PCR mediated amplification, which allowed the sequencing of the genomic regions flanking Tos17 insertions. This analysis was carried out in a collection of 47 A-genome Oryza species accessions and 202 accessions of a core collection of Oryza sativa L. representative of the diversity of the species. Our Southern hybridization results show that Tos17 is present in all the accessions of the A-genome Oryza species, except for the South American species O. glumaepatula and the African species O. glaberrima and O. breviligulata. In O. sativa, the number of putative copies of Tos17 per accession ranged from 1 to 11 and multivariate analysis based on presence/absence of putative copies yielded a varietal clustering which is consistent with the isozyme classification of rice. Adapter PCR amplification and sequencing of flanking regions of Tos17 insertions in A-genome species other than O. sativa, followed by anchoring on the Nipponbare genome sequence, revealed 13 insertion sites of Tos17 in the surveyed O. rufipogon and O. longistaminata accessions, including one shared by both species. In O. sativa, the same approach revealed 25 insertions in the 6 varietal groups. Four insertion sites located on chromosomes 1, 2, 10, and 11 were found orthologous in O. rufipogon and O. sativa. The chromosome 1 insertion was also shared between O. rufipogon and O. longistaminata. The presence of Tos17 at three insertion sites was confirmed by retrotransposon-based insertion polymorphism (RBIP) in a sample of O. sativa accessions. The first insertion, located on chromosome 3 was only found in two japonica accessions from the Bhutan region while the second insertion, located on chromosome 10 was specific to the varietal groups 1, 2, and 5. The third insertion located on chromosome 7 corresponds to the only insertion shown active in rice so far, notably in cv. Nipponbare, where it has been extensively used for insertion mutagenesis. This copy was only found in a few varieties of the japonica group 6 and in one group 5 accession. Taken together, these results confirm that Tos17 was probably present in the ancestor of A-genome species and that some copies of the element remained active in some Oryza lineages--notably in O. rufipogon and O. longistaminata--as well as in the indica and japonica O. sativa L. lineages.