Domestication to Crop Improvement: Genetic Resources for Sorghum and Saccharum (Andropogoneae)

Dillon, Sally L; Shapter, Frances M; Henry, Robert J.; Cordeiro, Giovanni M; Izquierdo, Liz; Lee, L Slade

doi:10.1093/aob/mcm192

Cited by 246 publications

(172 citation statements)

References 108 publications

(133 reference statements)

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“…Both D. saccharalis and D. lineolata were abundant on sorghum in the dry season, with nearly twice as many larvae of D. lineolata collected from sorghum as on were collected on corn. Diatraea lineolata is native to the Western Hemisphere and has had a much longer association with corn than with sorghum, which was introduced from Africa in the mid‐1800s (Dillon et al., 2007). The association of Diatraea spp.…”

Section: Discussionmentioning

confidence: 99%

Host‐plant associated genetic divergence of two Diatraea spp. (Lepidoptera: Crambidae) stemborers on novel crop plants

Joyce

Chicas

Cervantes

et al. 2016

Ecology and Evolution

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Diatraea lineolata and Diatraea saccharalis (Lepidoptera: Crambidae) are moths with stemboring larvae that feed and develop on economically important grasses. This study investigated whether these moths have diverged from a native host plant, corn, onto introduced crop plants including sorghum, sugarcane, and rice. Diatraea larvae were collected from these four host plants throughout the year in El Salvador and were reared on artificial diet until moths or parasitoids emerged. Adult moths were subsequently identified to species. Amplified fragment length polymorphisms (AFLPs) and mitochondrial DNA cytochrome oxidase I (COI) were used to examine whether or not there was genetic divergence of D. lineolata or D. saccharalis populations on the four host plants. Percent parasitism was also determined for each moth on its host plants. D. lineolata was collected from corn in the rainy season and sorghum in the dry season. D. saccharalis was most abundant on sugarcane in the rainy season and sorghum in the dry season. The AFLP analysis found two genetically divergent populations of both D. lineolata and D. saccharalis. Both moths had high levels of parasitism on their dominant host plant in the rainy season, yet had low levels of parasitism on sorghum in the dry season. The presence of two genotypes of both Diatraea spp. on sorghum suggest that host‐associated differentiation is occurring on this novel introduced crop plant.

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Section: Discussionmentioning

confidence: 99%

Host‐plant associated genetic divergence of two Diatraea spp. (Lepidoptera: Crambidae) stemborers on novel crop plants

Joyce

Chicas

Cervantes

et al. 2016

Ecology and Evolution

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“…hybrids, 2n = 100-130) are heterozygous aneupolyploid derivatives of interspecific hybrids primarily involving Saccharum officinarum L. and S. spontaneum L., with contributions from S. barberi Jeswiet, S. sinense Roxb., and S. robustum Brandes and Jeswiet ex Grassl (Dillon et al, 2007). The complex genomic structure makes sugarcane a difficult subject for genetic research, particularly in classical studies.…”

Section: Introductionmentioning

confidence: 99%

Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

Lu¹,

Zhou²,

Pan³

et al. 2015

Genet. Mol. Res.

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ABSTRACT.No information is available on segregation analysis of DNA markers involving both pollen and self-progeny. Therefore, we used capillary electrophoresis-and fluorescence-based DNA fingerprinting together with single pollen collection and polymerase chain reaction (PCR) to investigate simple sequence repeat (SSR) marker segregation among 964 single pollens and 288 self-progenies (S 1 ) of sugarcane cultivar LCP 85-384. Twenty SSR DNA fragments (alleles) were amplified by five polymorphic SSR markers. Only one non-parental SSR allele was observed in 2392 PCRs. SSR allele inheritance was in accordance with Mendelian laws of segregation and independent assortment. Highly significant correlation coefficients were found between frequencies of observed and expected genotypes in pollen and S 1 populations. Within the S 1 population, the most frequent genotype of each SSR marker was the parental genotype of the same marker. The number of genotypes was higher in pollen than S 1 population. PIC values of the five SSR markers were greater in pollen than S 1 populations. Eleven of 20 SSR alleles (55%) were segregated in accordance with Mendelian segregation ratios expected from pollen and S 1 populations of a 2n = 10x polyploid. Six of 20 SSR alleles were segregated in a 3:1 (presence:absence) ratio and were simplex markers. Four and one alleles were segregated in 77:4 and 143:1 ratios and considered duplex and triplex markers, respectively. Segregation ratios of remaining alleles were unexplainable. The results provide information about selection of crossing parents, estimation of seedling population optimal size, and promotion of efficient selection, which may be valuable for sugarcane breeders.

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“…Sorghum is the most closely related species to sugarcane (Grivet et al, 1994, Dillon et al, 2007. The sorghum genome sequencing project was initiated and completed in 2007, with the total genome size of ~730 Mb, and 34,496 protein-coding loci, at the coverage of 8.5x…”

Section: Sorghum Bicolor Genome As the Closest Related Reference Genomementioning

confidence: 99%

Analysis of genes controlling biomass traits in the genome of sugarcane (Saccharum spp. hybrids)

Hoang¹

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Sugarcane (Saccharum spp. hybrids) is a leading industrial crop in tropical and subtropical regions worldwide. More recently, sugarcane has been selected as a key feedstock for biofuels due to its rapid growth, high fiber content and favorable energy input/output ratio.Breeding sugarcane varieties with biomass for efficient conversion to biofuels can be optimized by understanding the genetic control of biomass composition. However, the genetic analysis of these traits is hindered by the genomic complexity, and the limited availability of a reference genome. The aims of this project were: the development of a high-throughput profiling method for rapid screening of the key biomass traits in a sugarcane population; the construction of a new full-length transcriptome reference database; and the identification of transcripts associated with sugar and fiber accumulation in sugarcane.For the screening of genotypes, newly developed predictive models employing nearinfrared (NIR) spectral analysis, coupled with the high performance liquid chromatography (HPLC), were shown to allow high-throughput profiling of major components in the fiber and sugar fractions in sugarcane biomass. Contrasting genotypes of low fiber and high fiber (minimum of ~29% and maximum of 61% total dry biomass) were identified amongst 331 samples from 186 sugarcane genotypes. The population studied exhibited a wide range of fiber/sugar ratio, from 0.4 (as low as that of the typical commercial sugarcane variety) to 2.2 (similar to that of energy-cane). In addition, the lignin content (the central factor in the biomass recalcitrance) ranged from 6 to 14% of the total dry biomass. To aid genotyping, a new sugarcane transcriptome (termed as SUGIT database) was constructed using PacBio full-length isoform sequencing (Iso-Seq), and a cDNA library derived from 22 diverse sugarcane genotypes, of the key tissues (leaf, internode and root), at different developmental stages (from immature to mature). Comparative analysis showed that this new SUGIT database included more full-length transcripts, longer predicted transcripts, and higher average length of the largest 1,000 proteins, compared to a de novo assembly from Illumina RNA-Seq short-read data from the same sample set. The annotation suggested that the majority (~94%) of the SUGIT database was from coding RNAs, while a very small proportion (~2%) could be long non-coding RNAs. About 70-82% of the RNASeq reads from different tissues mapped back to the SUGIT database, suggesting that it represented well the targeted tissues, while about 69% of this database was aligned with the sorghum genome, confirming the high conservation of orthologs in the genic regions of ii the two genomes. Applying the SUGIT database to differential expression analysis (FDR, false discovery rate corrected p-value <0.05), 1,649 transcript isoforms were identified as being differentially expressed between the young and mature tissues in the sugarcane plant, while 555 transcript isoforms were differentially expressed between th...

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Domestication to Crop Improvement: Genetic Resources for Sorghum and Saccharum (Andropogoneae)

Cited by 246 publications

References 108 publications

Host‐plant associated genetic divergence of two Diatraea spp. (Lepidoptera: Crambidae) stemborers on novel crop plants

Host‐plant associated genetic divergence of two Diatraea spp. (Lepidoptera: Crambidae) stemborers on novel crop plants

Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

Analysis of genes controlling biomass traits in the genome of sugarcane (Saccharum spp. hybrids)

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