Hybrid‐derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy

Imaizumi, Toshiyuki; Kawahara, Yoshihiro; Auge, Gabriela Alejandra

doi:10.1111/mec.16709

Cited by 4 publications

(4 citation statements)

References 81 publications

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“…In summary, the genome scan showed that aus-indica hybrid weeds can retain an optimal combination of traits and loci from both parents, which is in line with recent results of the stabilization of genomic regions associated with seed dormancy in hybrids between weedy and cultivated rice in Japan (Imaizumi et al, 2022).…”

Section: Signatures Of Adaptation In Argentinian Weedy Ricesupporting

confidence: 84%

Adaptive introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice

Presotto,

Hernández,

Vercellino

et al. 2023

Preprint

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Weedy rice, a pervasive and troublesome weed found across the globe, has often evolved through feralization of rice cultivars. In the South American Southern Cone region, rice breeding has a contemporary history and weedy rice has been reported as an important constraint since early 1970s; however the origin and genetic composition of Argentinian weedy rice has not been explored so far. To study this, we used genotyping-by-sequencing to generate genome-wide single nucleotide polymorphisms (SNPs) and compared Argentinian weedy rice with whole-genome data from strains, rice cultivars and wild rice accessions from regions worldwide. In addition, we conducted a comprehensive seed and phenological characterization, and performed an herbicide resistance screening, taking into account mutations in the ALS gene observed in the Argentinian weedy rice collection. Our results revealed large variability in seed traits and flowering time in Argentinian weedy rice. Additionally, most strains were resistant to ALS-inhibiting herbicides with a high frequency of the ALS mutation (A122T), which is also present in Argentinian rice cultivars. Cultivated rice varieties in Argentina belonged to the three major groups: japonica, indica and aus. In contrast, Argentinian weedy rice strains were mostly aus and aus-indica hybrids, resembling cultivars and weedy rice strains from the Southern Cone region. Our findings suggest that Argentinian weedy rice descends from aus weeds, presumably from the United States, which contemporaneously hybridized with local indica cultivars. The observed genetic similarities within the Southern Cone region can be attributed to the continuous exchange of breeding germplasm and cultivars, which, in turn, facilitated the dissemination of weedy rice strains.

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Section: Signatures Of Adaptation In Argentinian Weedy Ricesupporting

confidence: 84%

Adaptive introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice

Presotto,

Hernández,

Vercellino

et al. 2023

Preprint

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“…In summary, the genome scan showed that aus-indica admixed weeds can retain an optimal combination of traits and loci from both parents, which is in line with recent results of the stabilization of genomic regions associated with seed dormancy in hybrids between weedy and cultivated rice in Japan (Imaizumi et al, 2022).…”

Section: Herbicide Resistance Helps To Understand the Origin Of Argen...supporting

confidence: 84%

Introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice

Presotto,

Hernández,

Vercellino

et al. 2024

Molecular Ecology

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Weedy rice, a pervasive and troublesome weed found across the globe, has often evolved through fertilization of rice cultivars with little importance of crop‐weed gene flow. In Argentina, weedy rice has been reported as an important constraint since the early 1970s, and, in the last few years, strains with herbicide‐resistance are suspected to evolve. Despite their importance, the origin and genetic composition of Argentinian weedy rice as well its adaptation to agricultural environments has not been explored so far. To study this, we conducted genotyping‐by‐sequencing on samples of Argentinian weedy and cultivated rice and compared them with published data from weedy, cultivated and wild rice accessions distributed worldwide. In addition, we conducted a phenotypic characterization for weedy‐related traits, a herbicide resistance screening and genotyped accessions for known mutations in the acetolactate synthase (ALS) gene, which confers herbicide resistance. Our results revealed large phenotypic variability in Argentinian weedy rice. Most strains were resistant to ALS‐inhibiting herbicides with a high frequency of the ALS mutation (A122T) present in Argentinian rice cultivars. Argentinian cultivars belonged to the three major genetic groups of rice: japonica, indica and aus while weeds were mostly aus or aus‐indica admixed, resembling weedy rice strains from the Southern Cone region. Phylogenetic analysis supports a single origin for aus‐like South American weeds, likely as seed contaminants from the United States, and then admixture with local indica cultivars. Our findings demonstrate that crop to weed introgression can facilitate rapid adaptation to agriculture environments.

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“…As such, introgression is one of the driving forces for increasing genetic diversity and promoting adaptive evolution [3]. At present, many known gene introgression events involve adaptation [2], which is now known as adaptive introgression and has been found in plants [3,4], humans [5,6] and animals [7,8]. Hybridization is a method commonly used to breed new cultivars with desirable traits between wild and domesticated species in plant breeding [9,10].…”

Section: Introductionmentioning

confidence: 99%

Population Genomics Unravels the Characteristic Relationship between Introgression and Geographical Distribution in Upland Cotton

Shen

Cao²,

Zhang

et al. 2023

Agronomy

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Introgression is an important driver of new genetic variation that increases species and genetic diversity. However, the relationship between introgression and geographic distribution of upland cotton is still unclear. Herein, we explored geographically comprehensive genomic data based on 890 upland cotton accessions to decipher the degree of introgression between different geographic distributions and its effect on selection and fiber quality. We found introgression intervals to exist across different geographic distributions. Introgression is affected by the similarity of the environment in which they live, and those with similar ecological environments tend to share the same introgression area. Introgression is affected by artificial selection. A genome-wide association study (GWAS) meta-analysis was performed with 6 fiber traits and identified 261 quantitative trait loci (QTLs). We found that 67 QTLs had introgression signals, and the genome interval size was 118.81 Mb, while 123 QTLs had selection signals, and the genomic interval was 28.38 Mb. These results provide insights into the population-scaled introgression landscape, suggesting that introgression contributed to the cotton genetic improvement, which provides a useful reference for studying intraspecific introgressions from different geographical distributions in other species.

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Hybrid‐derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy

Cited by 4 publications

References 81 publications

Adaptive introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice

Adaptive introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice

Introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice

Population Genomics Unravels the Characteristic Relationship between Introgression and Geographical Distribution in Upland Cotton

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