Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization Events

Sharma, Anupma; Song, Jinjin; Lin, Qingfan; Singh, Ratnesh; Ramos, Ninfa; Wang, Kai; Zhang, Jisen; Ming, Ray; Yu, Qingyi

doi:10.3389/fpls.2018.01414

Cited by 5 publications

(2 citation statements)

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“…spontaneum, resulting in an octoploid with ten basic sets of chromosomes (2n=8x=80) (Sharma et al, 2018;Vilela et al, 2017;Zhang et al, 2021a). In support of this idea, a recent study which combined these two species to create a mosaic monoploid reference genome for Saccharum hybrid species reported that polyploidization in these species occurred after the divergence from sorghum (Garsmeur et al, 2018).…”

Section: Discussionmentioning

confidence: 90%

Dissecting the genetic basis of carbohydrate partitioning in maize and sugarcane

Dhungana¹

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[EMBARGOED UNTIL 6/1/2023] Carbohydrate partitioning, the process by which carbohydrates synthesized in the photosynthetic source tissues (mature leaves) are mobilized to non-photosynthetic (sink) tissues, such as roots, seeds, and developing organs is crucial for plant growth, development, and yield. Various physiological, biochemical, and anatomical studies have addressed this process, but the genetic control of carbohydrate partitioning is still not well understood. The main purpose of this dissertation is to elucidate aspects of the genetic control of carbohydrate partitioning in maize and sugarcane. Chapter 1 summarizes our current knowledge of phloem loading in grasses, the principal families of sugar transporters involved in sucrose transport, and novel mechanisms by which the activities of these sugar transporters are modulated. It also elaborates some of the recent discoveries in some eudicot species. Chapter 2 describes the genome of the wild ancestor of sugarcane (Saccharum spontaneum) and presents some ideas about the genes that may regulate sugar storage in the modern sugarcane varieties. For this study, I annotated Sucrose Transporters (SUTs) and Tonoplast Sugar Transporters (TSTs) in the S. spontaneum genome. Similarly, Chapter 3 describes the sugar transporter families; SUTs and TSTs in low (Saccharum spontaneum) and high sugar accumulating (Saccharum officinarum) sugarcane species and takes a comparative genomics approach to understand the ability of modern sugarcane cultivars to store huge amounts of sugars in their stem. Chapter 4 describes the characterization and cloning of maize carbohydrate partitioning defective13 (cpd13) and carbohydrate partitioning defective35 (cpd35) mutants, whereas Chapter 5 describes the characterization and progress towards cloning of carbohydrate partitioning defective60 (cpd60) and carbohydrate partitioning defective87 (cpd87) mutants. All of these mutants are recessive and contribute to carbohydrate hyperaccumulation in the mature leaves of the mutant due to reduced sucrose export. The cpd13 and cpd35 mutations affect a Dna-J-thioredoxin-like protein, which is hypothesized to be involved in processing of proteins and have chaperone-like activities. The cpd60 and cpd87 mutations result in ectopic lignin in the phloem of mature leaves, but the mechanism and the gene involved remain to be identified. Chapter 6 summarizes the discoveries made in the previous chapters and presents future research directions. Appendix A is a research article that I collaborated on and contributed to the measurement of non-structural carbohydrates in very oil yellow1 (vey1) leaves introgressed to B73 and Mo17 inbred lines. Collectively, the research presented here has enhanced our understanding of the genetic control of carbohydrate partitioning in maize and sugarcane. These studies establish the foundations for future experiments to determine the genetic architecture controlling carbohydrate partitioning in plants.

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Section: Discussionmentioning

confidence: 90%

Dissecting the genetic basis of carbohydrate partitioning in maize and sugarcane

Dhungana¹

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“…Permitem também localizar regiões codificadores de proteínas e identificar segmentos conservados, possibilitando o estudo dos padrões evolutivos de espécies relacionadas [22,[26][27][28][29]. Pesquisas em genômica comparativa foram reportadas em diversas espécies vegetais, por exemplo, as realizadas entre Brassica oleracea e Arabidopsis thaliana [30], Zea mays e A. thaliana [31], Fragaria e outras espécies do clado das Rosideas [32], Solanum lycopersicum e S. tuberosum [33], Oryza sativa e Ananas comosus [34], Glycine soja e outras 9 espécies de Glicine [35], Saccharum officinarum e S. spontaneum [36], entre outras.…”

Section: Introductionunclassified

Análise comparativa de regiões microssintênicas entre >i<Passiflora edulis>/i< e as Malpighiales >i<Populus trichocarpa>/i< e >i<Manihot esculenta>/i<

Reátegui¹,

Carmen²

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Sequencing vs. amplification for the estimation of allele dosages in sugarcane (Saccharum spp.)

Jaimes,

Londoño,

Saavedra‐Diaz

et al. 2024

Appl Plant Sci

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PremiseDetecting single‐nucleotide polymorphisms (SNPs) in a cost‐effective way is fundamental in any plant breeding pipeline. Here, we compare three genotyping techniques for their ability to reproduce the allele dosage of SNPs of interest in sugarcane (Saccharum spp.).MethodsTo identify a reproducible technique to estimate allele dosage for the validation of SNP markers, the correlation between Flex‐Seq, kompetitive allele‐specific PCR (KASP), and genotyping‐by‐sequencing and restriction site–associated DNA sequencing (GBS+RADseq) was determined for a set of 76 SNPs. To find alternative methodologies for allele dosage estimation, the KASP and Flex‐Seq techniques were compared for the same set of SNPs. For the three techniques, a population of 53 genotypes from the diverse sugarcane panel of the Centro de Investigación de la Caña de Azúcar (Cenicaña), Colombia, was selected.ResultsThe average Pearson correlation coefficients between GBS+RADseq and Flex‐Seq, GBS+RADseq and KASP, and Flex‐Seq and KASP were 0.62 ± 0.27, 0.38 ± 0.27, and 0.38 ± 0.30, respectively.DiscussionFlex‐Seq reproduced the allele dosages determined using GBS+RADseq with good levels of precision because of its depth of sequencing and ability to target specific positions in the genome. Additionally, Flex‐Seq outperformed KASP by allowing the conversion of a higher number of SNPs and a more accurate estimation of the allele dosage. Flex‐Seq has therefore become the genotyping methodology of choice for marker validation at Cenicaña.

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Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization Events

Cited by 5 publications

References 57 publications

Dissecting the genetic basis of carbohydrate partitioning in maize and sugarcane

Dissecting the genetic basis of carbohydrate partitioning in maize and sugarcane

Análise comparativa de regiões microssintênicas entre >i<Passiflora edulis>/i< e as Malpighiales >i<Populus trichocarpa>/i< e >i<Manihot esculenta>/i<

Sequencing vs. amplification for the estimation of allele dosages in sugarcane (Saccharum spp.)

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