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Genetics in Rice

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A special issue of Plants (ISSN 2223-7747).

Deadline for manuscript submissions: closed (31 December 2019) | Viewed by 41432

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Prof. Dr. Katsuyuki Ichitani

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Guest Editor

Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
Interests: reproductive barrier; disease resistance; varietal differentiation; genetics of agronomic trait

Prof. Ryuji Ishikawa

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Guest Editor

Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
Interests: wild rice resources; landrace resources for rice breeding; genes involving to morphological traits; domestication

Special Issue Information

Dear Colleagues,

Rice feeds more than half of the world population. Its small genome size and ease in transformation have made rice the model crop in plant physiology and genetics. Molecular as well as Mendelian, forward as well as reverse genetics collaborate with each other to expand rice genetics. Syntety of rice with other grasses such as wheat, barley and maize has helped accelerate their genomic studies.

The wild relatives of rice belonging to the genus Oryza are distributed in Asia, Africa, Latin America and Oceania. Phenotypic and genetic diversity among them contributes to their adaptation to a wide range of environments. They are good sources for the study of domestication and adaptation.

Rice is the first crop whose whole genome was sequenced. With the help of the reference genome of Nipponbare and the advent of the next generation sequencer, study of the rice genome has been accelerated. Now 3000 (3K) cultivar genome information, the pangenome information comprising the whole genes among rice as a species, and the genomes of wild relatives of rice are available.

The mining of DNA polymorphism has permitted map-based cloning, QTL analysis, GWAS, and the production of many kinds of experimental lines such as recombinant inbred lines, backcross inbred lines, and chromosomal segment substitution lines. The genetics of agronomic traits and pest resistance has led to the breeding of elite rice cultivars.

Inter- and intraspecific hybridization among Oryza species has opened the door to various levels of reproductive barriers ranging from prezygotic—e.g., hybrid sterility, male sterility—to postzygotic—e.g., hybrid weakness, hybrid breakdown.

This Special Issue will welcome papers on genetic studies of rice and its relatives utilizing the rich genetic resources and/or rich genome information described above.

Prof. Katsuyuki Ichitani
Prof. Ryuji Ishikawa
Guest Editors

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Keywords

gene mapping
genetic interaction
varietal differentiation
genomics
genetic resources

Published Papers (11 papers)

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25 pages, 4186 KiB

Open AccessArticle

In Silico Identification of QTL-Based Polymorphic Genes as Salt-Responsive Potential Candidates through Mapping with Two Reference Genomes in Rice

by Buddini Abhayawickrama, Dikkumburage Gimhani, Nisha Kottearachchi, Venura Herath, Dileepa Liyanage and Prasad Senadheera

Plants 2020, 9(2), 233; https://doi.org/10.3390/plants9020233 - 11 Feb 2020

Cited by 7 | Viewed by 3682

Abstract

Recent advances in next generation sequencing have created opportunities to directly identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while 1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected with InDels, tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and Os12g0624200 were found in the known salinity tolerant donor varieties. Our findings on different haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based breeding studies. Full article

(This article belongs to the Special Issue Genetics in Rice)

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15 pages, 826 KiB

Open AccessArticle

Molecular and Morphological Divergence of Australian Wild Rice

by Dinh Thi Lam, Katsuyuki Ichitani, Robert J. Henry and Ryuji Ishikawa

Plants 2020, 9(2), 224; https://doi.org/10.3390/plants9020224 - 10 Feb 2020

Cited by 4 | Viewed by 2552

Abstract

Two types of perennial wild rice, Australian Oryza rufipogon and a new taxon Jpn2 have been observed in Australia in addition to the annual species Oryza meridionalis. Jpn2 is distinct owing to its larger spikelet size but shares O. meridionalis-like morphological features including a high density of bristle cells on the awn surface. All the morphological traits resemble O. meridionalis except for the larger spikelet size. Because Jpn2 has distinct cytoplasmic genomes, including the chloroplast (cp), cp insertion/deletion/simple sequence repeats were designed to establish marker systems to distinguish wild rice in Australia in different natural populations. It was shown that the new taxon is distinct from Asian O. rufipogon but instead resembles O. meridionalis. In addition, higher diversity was detected in north-eastern Australia. Reproductive barriers among species and Jpn2 tested by cross-hybridization suggested a unique biological relationship of Jpn2 with other species. Insertions of retrotransposable elements in the Jpn2 genome were extracted from raw reads generated using next-generation sequencing. Jpn2 tended to share insertions with other O. meridionalis accessions and with Australian O. rufipogon accessions in particular cases, but not Asian O. rufipogon except for two insertions. One insertion was restricted to Jpn2 in Australia and shared with some O. rufipogon in Thailand. Full article

(This article belongs to the Special Issue Genetics in Rice)

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14 pages, 1870 KiB

Open AccessArticle

Allelic Differentiation at the E1/Ghd7 Locus Has Allowed Expansion of Rice Cultivation Area

by Hiroki Saito, Yutaka Okumoto, Takuji Tsukiyama, Chong Xu, Masayoshi Teraishi and Takatoshi Tanisaka

Plants 2019, 8(12), 550; https://doi.org/10.3390/plants8120550 - 28 Nov 2019

Cited by 9 | Viewed by 3591

Abstract

The photoperiod-insensitivity allele e1 is known to be essential for the extremely low photoperiod sensitivity of rice, and thereby enabled rice cultivation in high latitudes (42–53° north (N)). The E1 locus regulating photoperiod-sensitivity was identified on chromosome 7 using a cross between T65 and its near-isogenic line T65w. Sequence analyses confirmed that the E1 and the Ghd7 are the same locus, and haplotype analysis showed that the e1/ghd7-0a is a pioneer allele that enabled rice production in Hokkaido (42–45° N). Further, we detected two novel alleles, e1-ret/ghd7-0ret and E1-r/Ghd7-r, each harboring mutations in the promoter region. These mutant alleles alter the respective expression profiles, leading to marked alteration of flowering time. Moreover, e1-ret/ghd7-0ret, as well as e1/ghd7-0a, was found to have contributed to the establishment of Hokkaido varieties through the marked reduction effect on photoperiod sensitivity, whereas E1-r/Ghd7-r showed a higher expression than the E1/Ghd7 due to the nucleotide substitutions in the cis elements. The haplotype analysis showed that two photoperiod-insensitivity alleles e1/ghd7-0a and e1-ret/ghd7-0ret, originated independently from two sources. These results indicate that naturally occurring allelic variation at the E1/Ghd7 locus allowed expansion of the rice cultivation area through diversification and fine-tuning of flowering time. Full article

(This article belongs to the Special Issue Genetics in Rice)

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20 pages, 1840 KiB

Open AccessArticle

The Development and Characterization of Near-Isogenic and Pyramided Lines Carrying Resistance Genes to Brown Planthopper with the Genetic Background of Japonica Rice (Oryza sativa L.)

by Cuong D. Nguyen, Holden Verdeprado, Demeter Zita, Sachiyo Sanada-Morimura, Masaya Matsumura, Parminder S. Virk, Darshan S. Brar, Finbarr G. Horgan, Hideshi Yasui and Daisuke Fujita

Plants 2019, 8(11), 498; https://doi.org/10.3390/plants8110498 - 12 Nov 2019

Cited by 19 | Viewed by 5016

Abstract

The brown planthopper (BPH: Nilaparvata lugens Stål.) is a major pest of rice, Oryza sativa, in Asia. Host plant resistance has tremendous potential to reduce the damage caused to rice by the planthopper. However, the effectiveness of resistance genes varies spatially and temporally according to BPH virulence. Understanding patterns in BPH virulence against resistance genes is necessary to efficiently and sustainably deploy resistant rice varieties. To survey BPH virulence patterns, seven near-isogenic lines (NILs), each with a single BPH resistance gene (BPH2-NIL, BPH3-NIL, BPH17-NIL, BPH20-NIL, BPH21-NIL, BPH32-NIL and BPH17-ptb-NIL) and fifteen pyramided lines (PYLs) carrying multiple resistance genes were developed with the genetic background of the japonica rice variety, Taichung 65 (T65), and assessed for resistance levels against two BPH populations (Hadano-66 and Koshi-2013 collected in Japan in 1966 and 2013, respectively). Many of the NILs and PYLs were resistant against the Hadano-66 population but were less effective against the Koshi-2013 population. Among PYLs, BPH20+BPH32-PYL and BPH2+BPH3+BPH17-PYL granted relatively high BPH resistance against Koshi-2013. The NILs and PYLs developed in this research will be useful to monitor BPH virulence prior to deploying resistant rice varieties and improve rice’s resistance to BPH in the context of regionally increasing levels of virulence. Full article

(This article belongs to the Special Issue Genetics in Rice)

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14 pages, 947 KiB

Open AccessArticle

Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels

by Hayba Badro, Agnelo Furtado and Robert Henry

Plants 2019, 8(11), 481; https://doi.org/10.3390/plants8110481 - 07 Nov 2019

Cited by 8 | Viewed by 2908

Abstract

Due to the importance of the rice crop in Iraq, this study was conducted to determine the origin of the major varieties and understand the evolutionary relationships between Iraqi rice varieties and other Asian rice accessions that could be significant in the improvement of this crop. Five varieties of Oryza sativa were obtained from Baghdad/Iraq, and the whole genomic DNA was sequenced, among these varieties, Amber33, Furat, Yasmin, Buhooth1 and Amber al-Baraka. Raw sequence reads of 33 domesticated Asian rice accessions were obtained from the Sequence Read Archive (SRA-NCBI). The sequence of the whole chloroplast-genome was assembled while only the sequence of 916 concatenated nuclear-genes was assembled. The phylogenetic analysis of both chloroplast and nuclear genomes showed that two main clusters, Indica and Japonica, and further five sub-clusters based upon their ecotype, indica, aus, tropical-japonica, temperate-japonica and basmati were created; moreover, Amber33, Furat, Yasmin and Buhooth1 belonged to the basmati, indica and japonica ecotypes, respectively, where Amber33 was placed in the basmati group as a sister of cultivars from Pakistan and India. This confirms the traditional story that Amber was transferred by a group of people who had migrated from India and settled in southern Iraq a long time ago. Full article

(This article belongs to the Special Issue Genetics in Rice)

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9 pages, 1455 KiB

Open AccessArticle

Two SNP Mutations Turned off Seed Shattering in Rice

by Yu Zhang, Jiawu Zhou, Ying Yang, Walid Hassan Elgamal, Peng Xu, Jing Li, Yasser Z. El-Refaee, Suding Hao and Dayun Tao

Plants 2019, 8(11), 475; https://doi.org/10.3390/plants8110475 - 06 Nov 2019

Cited by 7 | Viewed by 3306

Abstract

Seed shattering is an important agronomic trait in rice domestication. In this study, using a near-isogenic line (NIL-hs1) from Oryza barthii, we found a hybrid seed shattering phenomenon between the NIL-hs1 and its recurrent parent, a japonica variety Yundao 1. The heterozygotes at hybrid shattering 1 (HS1) exhibited the shattering phenotype, whereas the homozygotes from both parents conferred the non-shattering. The causal HS1 gene for hybrid shattering was located in the region between SSR marker RM17604 and RM8220 on chromosome 4. Sequence verification indicated that HS1 was identical to SH4, and HS1 controlled the hybrid shattering due to harboring the ancestral haplotype, the G allele at G237T site and C allele at C760T site from each parent. Comparative analysis at SH4 showed that all the accessions containing ancestral haplotype, including 78 wild relatives of rice and 8 African cultivated rice, had the shattering phenotype, whereas all the accessions with either of the homozygous domestic haplotypes at one of the two sites, including 17 wild relatives of rice, 111 African cultivated rice and 65 Asian cultivated rice, showed the non-shattering phenotype. Dominant complementation of the G allele at G237T site and the C allele at C760T site in HS1 led to a hybrid shattering phenotype. These results help to shed light on the nature of seed shattering in rice during domestication and improve the moderate shattering varieties adapted to mechanized harvest. Full article

(This article belongs to the Special Issue Genetics in Rice)

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14 pages, 3085 KiB

Open AccessArticle

Rice Novel Semidwarfing Gene d60 Can Be as Effective as Green Revolution Gene sd1

by Motonori Tomita and Keiichiro Ishimoto

Plants 2019, 8(11), 464; https://doi.org/10.3390/plants8110464 - 30 Oct 2019

Cited by 9 | Viewed by 4893

Abstract

Gene effects on the yield performance were compared among promising semidwarf genes, namely, novel gene d60, representative gene sd1 with different two source IR8 and Jukkoku, and double dwarf combinations of d60 with each sd1 allele, in a Koshihikari background. Compared with the culm length of variety Koshihikari (mean, 88.8 cm), that of the semidwarf or double dwarf lines carrying Jukkoku_sd1, IR8_sd1, d60, Jukkoku_sd1 plus d60, or IR8_sd1 plus d60 was shortened to 71.8 cm, 68.5 cm, 65.7 cm, 48.6 cm, and 50.3 cm, respectively. Compared with the yield of Koshihikari (mean, 665.3 g/m²), that of the line carrying Jukkoku_sd1 allele showed the highest value (772.6 g/m², 16.1% higher than Koshihikari), while that of IR8_sd1, d60 and IR8_sd1 plus d60, was slightly decreased by 7.1%, 5.5%, and 9.7% respectively. The line carrying Jukkoku_sd1 also showed the highest value in number of panicles and florets/panicle, 16.2% and 11.1% higher than in Koshihikari, respectively, and these effects were responsible for the increases in yield. The 1000-grain weight was equivalent among all genetic lines. Except for the semidwarf line carrying Jukkoku_sd1, semidwarf line carrying d60 was equivalent to line carrying IR8_sd1in the yield of unpolished rice, and yield components such as panicle length, panicle number, floret number /panicle. Therefore, the semidwarfing gene d60 is one of the best possible choices in practical breeding. Full article

(This article belongs to the Special Issue Genetics in Rice)

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14 pages, 5559 KiB

Open AccessArticle

HWA1- and HWA2-Mediated Hybrid Weakness in Rice Involves Cell Death, Reactive Oxygen Species Accumulation, and Disease Resistance-Related Gene Upregulation

by Kumpei Shiragaki, Takahiro Iizuka, Katsuyuki Ichitani, Tsutomu Kuboyama, Toshinobu Morikawa, Masayuki Oda and Takahiro Tezuka

Plants 2019, 8(11), 450; https://doi.org/10.3390/plants8110450 - 25 Oct 2019

Cited by 12 | Viewed by 3347

Abstract

Hybrid weakness is a type of reproductive isolation in which F₁ hybrids of normal parents exhibit weaker growth characteristics than their parents. F₁ hybrid of the Oryza sativa Indian cultivars ‘P.T.B.7′ and ‘A.D.T.14′ exhibits hybrid weakness that is associated with the HWA1 and HWA2 loci. Accordingly, the aim of the present study was to analyze the hybrid weakness phenotype of the ‘P.T.B.7′ × ‘A.D.T.14′ hybrids. The height and tiller number of the F₁ hybrid were lower than those of either parent, and F₁ hybrid also exhibited leaf yellowing that was not observed in either parent. In addition, the present study demonstrates that SPAD values, an index correlated with chlorophyll content, are effective for evaluating the progression of hybrid weakness that is associated with the HWA1 and HWA2 loci because it accurately reflects degree of leaf yellowing. Both cell death and H₂O₂, a reactive oxygen species, were detected in the yellowing leaves of the F₁ hybrid. Furthermore, disease resistance-related genes were upregulated in the yellowing leaves of the F₁ hybrids, whereas photosynthesis-related genes tended to be downregulated. These results suggest that the hybrid weakness associated with the HWA1 and HWA2 loci involves hypersensitive response-like mechanisms. Full article

(This article belongs to the Special Issue Genetics in Rice)

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15 pages, 2076 KiB

Open AccessArticle

Segregation Distortion Observed in the Progeny of Crosses Between Oryza sativa and O. meridionalis Caused by Abortion During Seed Development

by Daiki Toyomoto, Masato Uemura, Satoru Taura, Tadashi Sato, Robert Henry, Ryuji Ishikawa and Katsuyuki Ichitani

Plants 2019, 8(10), 398; https://doi.org/10.3390/plants8100398 - 08 Oct 2019

Cited by 9 | Viewed by 3488

Abstract

Wild rice relatives having the same AA genome as domesticated rice (Oryza sativa) comprise the primary gene pool for rice genetic improvement. Among them, O. meridionalis and O. rufipogon are found in the northern part of Australia. Three Australian wild rice strains, Jpn1 (O. rufipogon), Jpn2, and W1297 (O. meridionalis), and one cultivated rice cultivar Taichung 65 (T65) were used in this study. A recurrent backcrossing strategy was adopted to produce chromosomal segment substitution lines (CSSLs) carrying chromosomal segments from wild relatives and used for trait evaluation and genetic analysis. The segregation of the DNA marker RM136 locus on chromosome 6 was found to be highly distorted, and a recessive lethal gene causing abortion at the seed developmental stage was shown to be located between two DNA markers, KGC6_10.09 and KGC6_22.19 on chromosome 6 of W1297. We name this gene as SEED DEVELOPMENT 1 (gene symbol: SDV1). O. sativa is thought to share the functional dominant allele Sdv1-s (s for sativa), and O. meridionalis is thought to share the recessive abortive allele sdv1-m (m for meridionalis). Though carrying the sdv1-m allele, the O. meridionalis accessions can self-fertilize and bear seeds. We speculate that the SDV1 gene may have been duplicated before the divergence between O. meridionalis and the other AA genome Oryza species, and that O. meridionalis has lost the function of the SDV1 gene and has kept the function of another putative gene named SDV2. Full article

(This article belongs to the Special Issue Genetics in Rice)

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13 pages, 2132 KiB

Open AccessArticle

Identification of Anther Length QTL and Construction of Chromosome Segment Substitution Lines of Oryza longistaminata

by Takayuki Ogami, Hideshi Yasui, Atsushi Yoshimura and Yoshiyuki Yamagata

Plants 2019, 8(10), 388; https://doi.org/10.3390/plants8100388 - 29 Sep 2019

Cited by 7 | Viewed by 3275

Abstract

Life histories and breeding systems strongly affect the genetic diversity of seed plants, but the genetic architectures that promote outcrossing in Oryza longistaminata, a perennial wild species in Africa, are not understood. We conducted a genetic analysis of the anther length of O. longistaminata accession W1508 using advanced backcross quantitative trait locus (QTL) analysis and chromosomal segment substitution lines (CSSLs) in the genetic background of O. sativa Taichung 65 (T65), with simple sequence repeat markers. QTL analysis of the BC₃F₁ population (n = 100) revealed that four main QTL regions on chromosomes 3, 5, and 6 were associated to anther length. We selected a minimum set of BC₃F₂ plants for the development of CSSLs to cover as much of the W1508 genome as possible. The additional minor QTLs were suggested in the regional QTL analysis, using 21 to 24 plants in each of the selected BC₃F₂ population. The main QTLs found on chromosomes 3, 5, and 6 were validated and designated qATL3, qATL5, qATL6.1, and qATL6.2, as novel QTLs identified in O. longistaminata in the mapping populations of 94, 88, 70, and 95 BC₃F₄ plants. qATL3, qATL5, and qATL6.1 likely contributed to anther length by cell elongation, whereas qATL6.2 likely contributed by cell multiplication. The QTLs were confirmed again in an evaluation of the W1508ILs. In several chromosome segment substitution lines without the four validated QTLs, the anthers were also longer than those of T65, suggesting that other QTLs also increase anther length in W1508. The cloning and diversity analyses of genes conferring anther length QTLs promotes utilization of the genetic resources of wild species, and the understanding of haplotype evolution on the differentiation of annuality and perenniality in the genus Oryza. Full article

(This article belongs to the Special Issue Genetics in Rice)

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17 pages, 789 KiB

Open AccessReview

Advances in Molecular Genetics and Genomics of African Rice (Oryza glaberrima Steud)

by Peterson W. Wambugu, Marie-Noelle Ndjiondjop and Robert Henry

Plants 2019, 8(10), 376; https://doi.org/10.3390/plants8100376 - 26 Sep 2019

Cited by 11 | Viewed by 3815

Abstract

African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted. Full article

(This article belongs to the Special Issue Genetics in Rice)

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