scholarly journals High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice

2021 ◽  
Vol 12 ◽  
Author(s):  
Fei Li ◽  
Zhenyun Han ◽  
Weihua Qiao ◽  
Junrui Wang ◽  
Yue Song ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Genetic Map ◽  
Agronomic Traits ◽  
Rice Variety ◽  
Heading Date ◽  
High Density ◽  
Weedy Rice ◽  
Rice Breeding ◽  
Cultivated Rice ◽  
High Quality

Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F2 population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.

Weedy Rice Diversity in Southern Brazil

Weed Science ◽  
2021 ◽  
pp. 1-37
Author(s):  
Leonard Bonilla Piveta ◽  
José Alberto Noldin ◽  
Nilda Roma-Burgos ◽  
Vívian Ebeling Viana ◽  
Lariza Benedetti ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Flowering Time ◽  
Weed Management ◽  
Phenotypic Diversity ◽  
Weedy Rice ◽  
Phenotypic Traits ◽  
Southern Brazil ◽  
Variable Response ◽  
Cultivated Rice ◽  
Flowering Synchrony

Abstract Weedy rice (Oryza sativa L.) is one of the most troublesome weeds affecting rice (Oryza sativa L.) production in many countries. Weedy rice control is difficult in rice fields because the weed and crop are phenotypically and morphologically similar. Weedy rice can be a source of genetic diversity to cultivated rice. Thus, this study aimed to characterize the morphological diversity of weedy rice in Southern Brazil. Qualitative and quantitative traits of 249 accessions from eight rice growing mesoregions in Rio Grande do Sul (RS) and Santa Catarina (SC) states were analyzed. For each accession, 24 morphological descriptors (14 qualitative and 10 quantitative) were evaluated. All the 249 accessions from RS and SC are of indica lineage. Considering all the phenotypic traits evaluated, the accessions separated into 14 distinct groups. One of the largest groups consisted of plants that were predominantly tall and with green leaves, intermediate shattering, and variable in flowering time. Distinct subgroups exist within larger clusters, showing discernable phenotypic diversity within the main clusters. The variability in flowering time was high (77 to 110 d after emergence), indicating high potential for flowering synchrony with rice cultivars and, consequently, gene flow. This indicates the need to remove escapes when planting herbicide-resistant rice. Thus, weedy rice populations in Southern Brazil are highly diverse and this diversity could result in variable response to weed management.

Effect of rice establishment methods on weedy rice (Oryza sativa L.) infestation and grain yield of cultivated rice (O. sativa L.) in Sri Lanka

2014 ◽  
Vol 55 ◽  
pp. 42-49 ◽  
Author(s):  
Bhagirath S. Chauhan ◽  
Anuruddhika S.K. Abeysekera ◽  
Manoja S. Wickramarathe ◽  
Sakinda D. Kulatunga ◽  
Upali B. Wickrama
Keyword(s):  
Oryza Sativa ◽  
Sri Lanka ◽  
Grain Yield ◽  
Oryza Sativa L ◽  
Weedy Rice ◽  
Cultivated Rice

Phenotypic diversity of weedy rice (Oryza sativa f. spontanea) biotypes found in California and implications for management

Weed Science ◽  
2020 ◽  
Vol 68 (5) ◽  
pp. 485-495
Author(s):  
Elizabeth Karn ◽  
Teresa De Leon ◽  
Luis Espino ◽  
Kassim Al-Khatib ◽  
Whitney Brim-DeForest
Keyword(s):  
Oryza Sativa ◽  
Chlorophyll Content ◽  
Plant Height ◽  
Wild Rice ◽  
Early Growth ◽  
Weedy Rice ◽  
Phenotypic Traits ◽  
Growth Stages ◽  
Cultivated Rice ◽  
Leaf Pubescence

AbstractWeedy rice (Oryza sativa f. spontanea Rosh.) is an emerging weed of California rice (Oryza sativa L.) that has potential to cause large yield losses. Early detection of weedy rice in the field is ideal to effectively control and prevent the spread of this weed. However, it is difficult to differentiate weedy rice from cultivated rice during early growth stages due to the close genetic and phenotypic relatedness of cultivated rice and weedy rice. The objective of this study is to examine phenotypic variation in weedy rice biotypes from California and to identify traits that could be used to visually identify weedy rice infestations at early growth stages for effective management. Greenhouse experiments were conducted in 2017 and 2018 using five phenotypically distinct biotypes of weedy rice found in California, along with diverse cultivated, weedy, and wild rice types in a randomized complete block design. We measured variation for 13 phenotypic traits associated with weedy rice and conducted principal component analysis and factor analysis to identify important weedy traits. Most weedy rice individuals within a biotype clustered together by phenotypic similarity. Pericarp color, hull color, chlorophyll content, grain length, plant height, leaf pubescence, collar color, and leaf sheath color account for most of the observed variation. California weedy rice biotypes are phenotypically distinct from wild rice and from weedy rice from the southern United States in their combinations of seed phenotypes and vegetative characteristics. In comparison with the locally grown temperate japonica cultivars, California weedy rice tends to be taller, with lower chlorophyll content and a red pericarp. Weedy rice biotypes vary in seed shattering and seed dormancy. For weedy rice management, plant height and chlorophyll content are distinct traits that could be used to differentiate weedy rice from the majority of cultivated rice varieties in California during vegetative stages of rice growth.

Fine mapping of a gene causing hybrid pollen sterility between Yunnan weedy rice and cultivated rice (Oryza sativa L.) and phylogenetic analysis of Yunnan weedy rice

Planta ◽  
2009 ◽  
Vol 231 (3) ◽  
pp. 559-570 ◽  
Author(s):  
Yong Wang ◽  
Zheng Zheng Zhong ◽  
Zhi Gang Zhao ◽  
Ling Jiang ◽  
Xiao Feng Bian ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Oryza Sativa ◽  
Fine Mapping ◽  
Oryza Sativa L ◽  
Pollen Sterility ◽  
Weedy Rice ◽  
Cultivated Rice

scholarly journals A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq

PLoS ONE ◽  
2017 ◽  
Vol 12 (6) ◽  
pp. e0179717 ◽  
Author(s):  
Jun Wang ◽  
Zhilan Wang ◽  
Xiaofen Du ◽  
Huiqing Yang ◽  
Fang Han ◽  
...  
Keyword(s):  
Genetic Map ◽  
Qtl Analysis ◽  
Agronomic Traits ◽  
Foxtail Millet ◽  
High Density ◽  
Setaria Italica

scholarly journals Genome sequence of the model rice variety KitaakeX

2019 ◽  
Author(s):  
Rashmi Jain ◽  
Jerry Jenkins ◽  
Shengqiang Shu ◽  
Mawsheng Chern ◽  
Joel A. Martin ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Rice Plant ◽  
De Novo ◽  
Rice Variety ◽  
High Quality ◽  
Protein Coding ◽  
Genomic Variations ◽  
Protein Coding Genes ◽  
Gene Annotations ◽  
High Quality Genome

AbstractHere, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics.

scholarly journals Rapid PCD Process Promotes Early Maturity in Weedy Rice (Oryza sativa L. f. spontanea)

2020 ◽  
Author(s):  
Can Zhao ◽  
Wenrong Xu ◽  
Zheng Zhang ◽  
Lingchao Meng ◽  
Weimin Dai ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Oryza Sativa ◽  
Cell Viability ◽  
Grain Filling ◽  
Oxidative Enzymes ◽  
Weedy Rice ◽  
Oxygen Species ◽  
Cultivated Rice ◽  
Early Maturity ◽  
Grain Filling Period

Abstract Background: Shorter grain-filling period and rapid endosperm development contributes to early maturity in weedy rice (Oryza sativa L. f. spontanea). However, the differences in programmed cell death (PCD) process and anti-oxidative enzymes system in the caryopsis between weedy and cultivated rice are largely unexplored. Main Text: we selected four biotypes of weedy rice and associated cultivated rice (ACR, Oryza sativa) from different latitudes to conduct a common garden experiment. The difference of PCD process between weedy rice and ACR was compared by chemical staining, and the cell viability and nuclear morphometry of endosperm cells were observed by optical microscopy, and anti-oxidative enzymes activity were also measured during grain filling. We found that the PCD progress in weedy rice was more rapid and earlier than that in ACR. The percentage of degraded nuclei of weedy rice were 10%-83% higher than that of ACR. Endosperm cells in weedy rice lost cell viability 2-8 days earlier than that in ACR. The anti-oxidant enzymes activity of weedy rice were lower than that of ACR during grain filling. The ability of weedy rice to scavenge reactive oxygen species is weaker than that of ACR, which may contribute to the rapid PCD process in the endosperm cells of weedy rice. Conclusion: The rapid PCD process and weaker ability to scavenge reactive oxygen species in endosperm cells lead to the shorter grain-filling period of weedy rice.

scholarly journals Identification of fgr gene and preliminary evaluation for agronomic traits of pandan sticky rice variety (Oryza sativa L.)

2019 ◽  
Vol 02 ◽  
pp. 39-48
Author(s):  
Toan D. Pham
Keyword(s):  
Oryza Sativa ◽  
Agronomic Traits ◽  
Oryza Sativa L ◽  
Rice Variety ◽  
Rice Production ◽  
Molecular Techniques ◽  
High Yield ◽  
Preliminary Evaluation ◽  
Rice Varieties ◽  
Fgr Gene

Rice (Oryza sativa L.) is the most important food crop in Vietnam particularly in the Mekong Delta. Screening of good quality and high yield rice varieties are needed for rice production in Vietnam. The purpose of this study was to use molecular techniques to identify fgr gene and to evaluate preliminarily agronomic traits of pandan sticky rice variety. The results showed that this variety contained fgr gene. The fragrant allele was amplified by ESP - IFAP primers with a product of 255 bp in size. Similarly, evaluation of agronomic traits showed that the pandan sticky rice variety displayed many desirable characteristics such as plant height of 108 cm, panicle length of 25.6 cm, seed/panicle 135, 100-grain weight 2.07 g, pandan smell, level 2 of alkali digestion, gel consistency 93 mm. These results were useful information and could be applied for improving and providing pandan sticky rice variety for rice production.

scholarly journals IMPROVEMENT OF EARLY MATURITY IN RICE VARIETY BY MARKER ASSISTED BACKCROSS BREEDING OF Hd2 GENE

2014 ◽  
Vol 15 (2) ◽  
pp. 55
Author(s):  
Fatimah Fatimah ◽  
Joko Prasetiyono ◽  
Ahmad Dadang ◽  
Tasliah Tasliah
Keyword(s):  
Agronomic Traits ◽  
Rice Variety ◽  
Heading Date ◽  
Rice Production ◽  
Early Maturity ◽  
Breeding Lines ◽  
Early Maturing ◽  
Two Generations ◽  
Donor Parent ◽  
Marker Assisted Backcross Breeding

Early-maturing and high-yielding rice variety is very useful for increasing rice production in Indonesia. The aim of this research was to develop new lines of Indonesian rice containing Hd2 gene using Code variety as a recipient parent and Nipponbare variety as a donor parent through targetted MAB approach using RM1362 and RM7601 in chromosom 7 for foreground selection. After two generations of backcrossing, the positive alleles of Hd2 gene from Nipponbare had successfully trans-ferred into Code. The plant number CdNp_29 in BC2F2 popula-tion had the highest genome recovery of 82.7%. The twelve BC2F3 plants were selected for self-pollination to generate BC2F4. These selected lines that carried the Hd2 gene were screened in the greenhouse for the evaluation of heading date and agronomic traits. All improved lines had Hd2 gene similar to the donor parent Nipponbare. The heading date of the breeding lines ranged from 73 to 89 days (Code 85 days) or fill the third criterion of rice maturity that is 103-104 days compared to Code of 116-119 days, whereas their agronomic performances were similar with that of Code. Application of MABc for im-proving rice early maturity has accelerated the development and selection in early generation of superior lines having genetic background of Code. It is expected that the newly developed lines of Code will be utilized to increase rice production in Indonesia.

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