The Role of Standing Variation in the Evolution of Weedines Traits in South Asian Weedy Rice (<i>Oryza</i> spp.)

Huang, Zhongyung; Kelly, Shannon; Matsuo, Rika; Li, Linfeng; Li, Yaling; Olsen, Kenneth M.; Jia, Yulin; Caicedo, Ana L.

doi:10.1534/g3.118.200605

Cited by 21 publications

(27 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Weedy rice (Oryza sativa L.) is a widespread weed in cultivated rice (Oryza sativa L.) throughout the world that can cause severe yield losses (Fogliatto et al 2020b;Nadir et al 2017). The majority of O. sativa populations have been classified as belonging to the same species as cultivated rice and of having a red pericarp, which has led to them being referred to as "red rice" (Cao et al 2007;Cui et al 2016;Huang et al 2018). This weed has become widespread in many ricegrowing areas throughout the world as a consequence of increased adoption of direct rice seeding, mainly due to the scarce availability of low-cost labor (Delouche et al 2007;Ziska et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Relationship between weedy rice (Oryza sativa) infestation level and agronomic practices in Italian rice farms

et al. 2020

View full text Add to dashboard Cite

Weedy rice (Oryza sativa L.) is a troublesome rice (Oryza sativa L.) weed in Italy and in many other rice areas. The objective of this study was to correlate the O. sativa infestation level in northern Italy, the main European rice-growing area, with agricultural practices adopted by farmers by using data obtained from a farmer survey. In 2018 to 2019, a survey was carried out on 98 rice farms chosen to ensure different sizes, different cultivation practices, and variable degrees of O. sativa infestation. The following information was acquired: farm size; area cultivated with Clearfield® varieties; the most-adopted agronomic practices (type of tillage, crop rotation, type of sowing, water management, origin of seeds, adoption of stale seedbed, use of imazamox, presence of O. sativa resistant to imazamox); and level of O. sativa infestation: low (≤5 plants m−2), medium (>5 to 20 plants m−2), and high (>20 plants m−2). The data were analyzed through descriptive statistics and ordinal logistic regression to determine which agronomic practices influenced the level of O. sativa infestation. Farm clustering was also determined through two-step cluster analysis. Rice was cultivated as a monocrop and mainly sown in water, using purchased seeds, in plowed fields. More than half of the farms used the stale seedbed practice, and 63% adopted Clearfield® varieties, while about 45% of the farms reported imazamox-resistant O. sativa. The ordinal logistic regression underlined that use of a stale seedbed was correlated with the infestation level of O. sativa, and the two-step cluster analysis showed that the farms were mainly grouped based on the use of this technique. Most of the farms that used a stale seedbed had higher O. sativa infestation than those that did not use it, meaning that this practice was mainly applied in zones where O. sativa infestations were more serious.

show abstract

Section: Introductionmentioning

confidence: 99%

Relationship between weedy rice (Oryza sativa) infestation level and agronomic practices in Italian rice farms

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Despite carrying the reduced-shattering allele, however, weedy rice strains are typically highly shattering, and the re-emergence of the shattering phenotype appears to have occurred through multiple compensatory mutations throughout the genome (Qi et al 2015;Li et al 2017). In Southeast Asia, some weedy rice strains carry the wild sh4 allele, a pattern consistent with adaptive introgression from local wild rice populations (Song et al 2014;Huang et al 2018).…”

Section: Introductionmentioning

confidence: 97%

“…For such traits, introgression from wild populations rather than crop varieties could be adaptive for allowing the weeds to persist and proliferate in agricultural fields. Comparisons of the distributions of crop versus wild alleles at multiple domestication genes can thus provide insights on patterns of adaptive introgression into weed populations from domesticated and wild relatives (Song et al 2014;Cui et al 2016;Huang et al 2018).…”

Section: Introductionmentioning

confidence: 99%

“…Comparative analyses of domestication genes and neutral markers have proved particularly insightful in evolutionary studies of weedy rice (Song et al 2014;Cui et al 2016;Huang et al 2018). These analyses have largely relied on 3 well-characterized rice domestication genes: sh4 (controlling loss of shattering in the crop), Rc (controlling loss of pericarp pigmentation and seed dormancy in the crop), and Bh4 (controlling loss of dark-pigmented hulls in the crop).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Wedger

Pusadee

Wongtamee

et al. 2019

Journal of Heredity

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…A number of identified genes know to contribute to the pigmentation of rice pericarp, among which a major factor is Rc , a bHLH protein involving in proanthocyanidin synthesis (Furukawa et al 2007 ; Sweeney et al 2006 ). Potentially descended from cultivated ancestors, the weedy traits that WR possesses are likely to be derived from standing variation in wild or cultivated rice (Huang et al 2018 ; Vigueira et al 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Explore the genetics of weedy traits using rice 3K database

Lin

et al. 2021

Bot Stud

View full text Add to dashboard Cite

Background Weedy rice, a conspecific weedy counterpart of the cultivated rice (Oryza sativa L.), has been problematic in rice-production area worldwide. Although we started to know about the origin of some weedy traits for some rice-growing regions, an overall assessment of weedy trait-related loci was not yet available. On the other hand, the advances in sequencing technologies, together with community efforts, have made publicly available a large amount of genomic data. Given the availability of public data and the need of “weedy” allele mining for a better management of weedy rice, the objective of the present study was to explore the genetic architecture of weedy traits based on publicly available data, mainly from the 3000 Rice Genome Project (3K-RGP). Results Based on the results of population structure analysis, we have selected 1378 individuals from four sub-populations (aus, indica, temperate japonica, tropical japonica) without admixed genomic composition for genome-wide association analysis (GWAS). Five traits were investigated: awn color, seed shattering, seed threshability, seed coat color, and seedling height. GWAS was conducted for each sub-population × trait combination and we have identified 66 population-specific trait-associated SNPs. Eleven significant SNPs fell into an annotated gene and four other SNPs were close to a putative candidate gene (± 25 kb). SNPs located in or close to Rc were particularly predictive of the occurrence of seed coat color and our results showed that different sub-populations required different SNPs for a better seed coat color prediction. We compared the data of 3K-RGP to a publicly available weedy rice dataset. The profile of allele frequency, phenotype-genotype segregation of target SNP, as well as GWAS results for the presence and absence of awns diverged between the two sets of data. Conclusions The genotype of trait-associated SNPs identified in this study, especially those located in or close to Rc, can be developed to diagnostic SNPs to trace the origin of weedy trait occurred in the field. The difference of results from the two publicly available datasets used in this study emphasized the importance of laboratory experiments to confirm the allele mining results based on publicly available data.

show abstract

The Role of Standing Variation in the Evolution of Weedines Traits in South Asian Weedy Rice (Oryza spp.)

Cited by 21 publications

References 41 publications

Relationship between weedy rice (Oryza sativa) infestation level and agronomic practices in Italian rice farms

Relationship between weedy rice (Oryza sativa) infestation level and agronomic practices in Italian rice farms

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

Explore the genetics of weedy traits using rice 3K database

Contact Info

Product

Resources

About