Special Issue "Genetics in Rice"

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

Deadline for manuscript submissions: 31 December 2019.

Special Issue Editors

Assoc. Prof. Katsuyuki Ichitani
E-Mail Website
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
E-Mail Website
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

Manuscript Submission Information

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Keywords

  • gene mapping
  • genetic interaction
  • varietal differentiation
  • genomics
  • genetic resources

Published Papers (3 papers)

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Research

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Open AccessArticle
Segregation Distortion Observed in the Progeny of Crosses Between Oryza sativa and O. meridionalis Caused by Abortion During Seed Development
Plants 2019, 8(10), 398; https://doi.org/10.3390/plants8100398 - 08 Oct 2019
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 [...] Read more.
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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Open AccessArticle
Identification of Anther Length QTL and Construction of Chromosome Segment Substitution Lines of Oryza longistaminata
Plants 2019, 8(10), 388; https://doi.org/10.3390/plants8100388 - 29 Sep 2019
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 [...] Read more.
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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Review

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Open AccessReview
Advances in Molecular Genetics and Genomics of African Rice (Oryza glaberrima Steud)
Plants 2019, 8(10), 376; https://doi.org/10.3390/plants8100376 - 26 Sep 2019
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 [...] Read more.
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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