Discordant Patterns of Introgression Suggest Historical Gene Flow into Thai Weedy Rice from Domesticated and Wild Relatives

2019 ◽  
Vol 110 (5) ◽  
pp. 601-609 ◽  
Author(s):  
Marshall J Wedger ◽  
Tonapha Pusadee ◽  
Anupong Wongtamee ◽  
Kenneth M Olsen
Keyword(s):  
Gene Flow ◽  
Ssr Markers ◽  
Wild Rice ◽  
Allelic Variation ◽  
Wild Relatives ◽  
Weedy Rice ◽  
Cultivated Rice ◽  
Crop Species ◽  
Global Food Security ◽  
North East

Abstract Weedy relatives of crop species infest agricultural fields worldwide, reducing harvests and threatening global food security. These weeds can potentially evolve and adapt through gene flow from both domesticated crop varieties and reproductively compatible wild relatives. We studied populations of weedy rice in Thailand to investigate the role of introgression from cultivated and wild rice in their evolution. We examined 2 complementary sources of genetic data: allelic variation at 3 rice domestication genes (Bh4, controlling hull color; Rc, controlling pericarp color and seed dormancy; and sh4, controlling seed shattering), and 12 previously published SSR markers. Sampling spanned 3 major rice growing regions in Thailand (Lower North, North East, and Central Plain) and included 124 cultivated rice accessions, 166 weedy rice accessions, and 98 wild rice accessions. Weedy rice strains were overall closely related to the cultivated varieties with which they co-occur. Domestication gene data revealed potential adaptive introgression of sh4 shattering alleles from wild rice. Introgression of potentially maladaptive rc crop alleles (conferring reduced dormancy) was also detected, with the frequency of the crop allele highest in northern populations. Although SSR markers also indicated introgression into weed populations from wild and cultivated rice, there was little overlap with domestication genes in the accessions showing admixed ancestry. This suggests that much of the introgression we detected at domestication genes most likely reflects past introgression rather than recent gene flow. This finding has implications for understanding long-term gene flow dynamics between rice and its weedy and wild relatives, including potential risks of transgene escape.

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.

Genome-wide genic SSR marker development for the endangered Dongxiang wild rice (Oryza rufipogon)

2016 ◽  
Vol 15 (6) ◽  
pp. 566-569
Author(s):  
Jiankun Xie ◽  
Meng Zhang ◽  
Jia Sun ◽  
Fantao Zhang
Keyword(s):  
Ssr Markers ◽  
Wild Rice ◽  
Pcr Amplification ◽  
Oryza Rufipogon ◽  
Sequencing Technology ◽  
Cultivated Rice ◽  
Genic Ssr ◽  
Genome Wide ◽  
Dongxiang Wild Rice ◽  
Simple Sequence

AbstractDongxiang wild rice (Oryza rufipogon, DXWR), one of the species of common wild rice, is regarded as an important genetic resource for the improvement of cultivated rice (Oryza sativa). Molecular markers are reliable tools that can greatly accelerate the breeding process and have been widely used in various species. In the present study, a total of 3681 genic simple sequence repeat (SSR) markers were developed for DXWR based on transcriptome sequencing technology. Additionally, 25 primer pairs were randomly selected and synthesized for the verification. Among them, 18 (72%) primer pairs were successfully amplified in PCR amplification with genomic DNA of DXWR and also had abundant polymorphisms between DXWR and cultivated rice. These novel genic SSR markers will enrich current genomic resources for DXWR, and provide an effective tool for genetic study and molecular marker assisted breeding for this valuable and endangered germplasm.

Mutations in the red rice ALS gene associated with resistance to imazethapyr

Weed Science ◽  
2005 ◽  
Vol 53 (5) ◽  
pp. 567-577 ◽  
Author(s):  
Satyendra N. Rajguru ◽  
Nilda R. Burgos ◽  
Vinod K. Shivrain ◽  
James McD. Stewart
Keyword(s):  
Gene Flow ◽  
Ssr Markers ◽  
Point Mutations ◽  
Acetolactate Synthase ◽  
Weedy Rice ◽  
Rice Cultivars ◽  
Red Rice ◽  
Coding Region ◽  
Gene Sequences ◽  
Herbicide Resistant

The introduction of Clearfield (CL) rice cultivars resistant to imidazolinone herbicides, acetolactate synthase (ALS) inhibitors, has raised concerns of gene flow to weedy rice genotypes collectively called “red rice” that infest rice-growing areas in the southern United States. This experiment was conducted to study hybridization between CL rice and red rice using simple sequence repeats (SSR) markers, identify mutations in the ALS gene of imazethapyr-resistant red rice, and to detect the introgression of the ALS-resistant gene from CL rice into red rice. Natural outcrossing experiments between CL rice and strawhull (SH) red rice were set up in Stuttgart, AR, in 2002 and 2003. Putative red rice hybrids were detected among volunteer plants in the following year. Hybridization was confirmed using SSR markers, and introgression of the resistant ALS gene from CL rice to red rice was detected by ALS gene sequencing. The ALS gene sequences of U.S. rice cultivars ‘Bengal’ and ‘Cypress’, SH red rice, CL rice (CL161), and imazethapyr-resistant red rice/CL rice hybrids were compared. Nucleotide sequences of the ALS gene from the rice cultivars were identical. Three point mutations were present in the SH red rice ALS gene coding region relative to Bengal/Cypress. One of these resulted in the substitution of Asp630for Glu630. The ALS gene sequences of confirmed hybrids were identical to that of the herbicide-resistant pollen source, CL161. We identified four ALS gene mutations in the herbicide-resistant red rice hybrids relative to the susceptible rice cultivars. One point mutation, resulting in a substitution of Ser653with Asn, was linked to ALS resistance in callus tissue derived from a Kinmaze rice line from Japan. The other three mutations (Ser186—Pro, Lys416—Glu, and Leu662—Pro) are novel. This experiment confirmed that gene flow from imidazolinone-resistant rice resulted in herbicide-resistant red rice plants.

scholarly journals The Possibility of Gene Flow Between Cultivated and Wild Rice in Ghana, A Review

2019 ◽  
Author(s):  
Gavers Kwasi Oppong ◽  
Belinda Akomeah ◽  
Isaac Tawiah ◽  
Maxwell Darko Asante
Keyword(s):  
Gene Flow ◽  
Transgenic Rice ◽  
Wild Rice ◽  
Field Trials ◽  
Cultivated Rice ◽  
Wild Rice Species ◽  
Gm Rice ◽  
Aa Genome ◽  
Autogamous Plant ◽  
Wild Oryza Species

Several transgenic rice lines have been developed and are currently under field trials around the world. There are future plans for the commercial release of transgenic rice into the environment. Rice is an autogamous plant and therefore not perceived to be a very high candidate for pollen mediated gene flow to wild and weedy relatives. However, in a tropical environment like Ghana, where sexually compatible wild Oryza species which belongs to the AA genome are present within the ecology of cultivated rice, the possibility of gene flow to wild species cannot be overlooked. There is little evidence on gene flow and its consequences on the wild rice species should they acquire useful genes through gene flow. This review discusses the chances of cultivated to wild rice gene flow in Ghana and the biosafety considerations that should be put in place before the commercial release of genetically modified (GM) rice.

scholarly journals Assessment of Genetic Diversity in Wild Rice of Eastern India Using SSR Markers

2017 ◽  
Vol 9 (6) ◽  
pp. 239
Author(s):  
Rosalin Swain ◽  
Shibani Mohapatra ◽  
Pritesh Roy ◽  
D. Swain ◽  
O. N. Singh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Wild Rice ◽  
West Bengal ◽  
Cultivated Rice ◽  
Morphological Variations ◽  
Aa Genome ◽  
Clustering Pattern ◽  
Genetic Diversity Study ◽  
Diversity Study

Wild rice is an important reservoir of valuable and useful genes. O. rufipogon and O. nivara contain AA genome andare the progenitor of cultivated rice which makes them compatible with the cultivated rice for cross breeding to incorporate the genes for stress tolerance. SSR markers were used to assess the extent of diversity of 26 accessions of O. rufipogon and O. nivara collected from different districts of Orissa, West Bengal and Tripura. The Principal Co-ordinate Analysis (PCA) clearly indicates the clustering pattern and inter-relationships among different accessions. Mantel Z-testexhibitedacorrelation between cophenetic matrix and Jaccards’ similarity coefficient in 26 accessions and 4 CRRI released varieties using 54 STMS (SSR) markers which showed significant correlation (r = 0.8249) between them. O. nivara accessions and O. rufipogon accessions were grouped different clusters. O. nivara collected from Midnapore is placed in different cluster. It is concluded that the SSR markers used were found to be equally informative for the genetic diversity study between and among the accessions of two wild species such as O. rufipogon and O. nivara collected from different locations of Orissa, West Bengal & Tripura. Highlysignificant morphological variations were also observed among O. nivara and O. rufipogon accessions.

Gene flow from glufosinate-resistant transgenic hybrid rice Xiang 125S/Bar68-1 to weedy rice and cultivated rice under different experimental designs

Euphytica ◽  
2015 ◽  
Vol 204 (1) ◽  
pp. 211-227 ◽  
Author(s):  
Guanghui Sun ◽  
Weimin Dai ◽  
Rongrong Cui ◽  
Sheng Qiang ◽  
Xiaoling Song
Keyword(s):  
Gene Flow ◽  
Hybrid Rice ◽  
Experimental Designs ◽  
Weedy Rice ◽  
Cultivated Rice

Collection of Wild Helianthus anomalus and deserticola Sunflower from the Desert Southwest USA

Helia ◽  
2016 ◽  
Vol 39 (65) ◽  
Author(s):  
Gerald J. Seiler ◽  
Laura Fredrick Marek
Keyword(s):  
Food Security ◽  
Genetic Resources ◽  
Germplasm Conservation ◽  
Initial Step ◽  
Wild Relatives ◽  
Crop Species ◽  
Global Food Security ◽  
Desert Southwest ◽  
Southwest Usa ◽  
Global Food

AbstractGenetic resources are the biological basis of global food security. Collection and preservation of wild relatives of important crop species such as sunflower provide the basic foundation to improve and sustain the crop. Acquisition through exploration is the initial step in the germplasm conservation process. There are 53 species of wild

Weedy Rice (Oryza spp.): What’s In a Name?

Weed Science ◽  
2021 ◽  
pp. 1-36
Author(s):  
Nilda Roma-Burgos ◽  
Maggie Pui San Sudo ◽  
Kenneth M. Olsen ◽  
Isabel Werle ◽  
Beng-Kah Song
Keyword(s):  
Oryza Sativa ◽  
Wild Rice ◽  
Weedy Rice ◽  
Ganges River ◽  
Cultivated Rice ◽  
Wild Progenitor ◽  
Wild Rice Species ◽  
Proper Name ◽  
Direct Seeded ◽  
The Ganges

Abstract There are two species of cultivated rice in the world - Oryza sativa L. from Asia and O. glaberrima from Africa. The former was domesticated from the wild progenitor, O. rufipogon and the latter from the African wild rice species O. barthii. The first known center of rice cultivation in China generated the O. sativa subspecies japonica. The indica subspecies arose from the second center of domestication in the Ganges River plains of India. Variants of domesticated lines and the continuous hybridization between cultivated varieties and the wild progenitor(s) resulted in weedy rice types. Some weedy types resemble the wild ancestor, but the majority of weedy rices today bear close resemblance to cultivated rice. Weedy rice accompanies rice culture and has increased in occurrence with the global shift in rice establishment from transplanting to direct-seeded, or dry-drill-seeded rice. Weedy rice (Oryza spp.) is the most-difficult-weed to control in rice, causing as much as 90% yield loss or abandonment of severely infested fields. The gene flow continuum between cultivar and weedy rice or wild relative, crop dedomestication, and regionalized adaptation has resulted in a myriad of weedy rice types. The complex lineage of weedy rice has resulted in confusion of weedy rice nomenclature. Two names are generally used for weedy rice – O. sativa L. and O. sativa f. spontanea. Genomic data shows that Oryza sativa L. applies to weedy rice populations derived from cultivated O. sativa whereas spontanea applies only to weedy types that primarily descended from O. rufipogon. Neither of these names apply to African weedy rice, which are of African wild rice, or O. glaberrima lineage. Therefore, unless the lineage of the weedy population in question is known, the proper name to use is the generalized name Oryza spp.

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