Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification

You, Qi; Yang, Xiping; Peng, Ze; Islam, Md. Rafikul; Sood, Sushma; Luo, Ziliang; Comstock, Jack C.; Xu, Liping; Wang, Jianping

doi:10.1007/s00122-019-03391-4

Cited by 44 publications

(29 citation statements)

References 71 publications

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“…In this study, two QTLs were identified for resistance against SCYLV, among them QTL qSCYLR79 associated with marker 3PAV3154 showed to be specific for SCYLV resistance (Islam et al, 2018). Recently, You et al (2019) developed an Axiom Sugarcane 100K single nucleotide polymorphism display and magnificently employed to develop the genetic map of sugarcane and to recognize the QTL linked with SCYLV resistance. This arrangement was used to genotype 469 sugarcane clones, having one F1 (parents: Green German and IND81-146), one selfing populations obtained from CP80-1827 and 11 different sugarcane stocks as controls.…”

Section: Next Generation Strategies For Management Of Scylvmentioning

confidence: 99%

Present Status and Future Management Strategies for Sugarcane Yellow Leaf Virus: A Major Constraint to the Global Sugarcane Production

et al. 2020

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Sugarcane yellow leaf virus (SCYLV) is a distinct member of the Polerovirus genus of the Luteoviridae family. SCYLV is the major limitation to sugarcane production worldwide and presently occurring in most of the sugarcane growing countries. SCYLV having high genetic diversity within the species and presently ten genotypes are known to occur based on the complete genome sequence information. SCYLV is present in almost all the states of India where sugarcane is grown. Virion comprises of 180 coat protein units and are 24-29 nm in diameter. The genome of SCYLV is a monopartite and comprised of single-stranded (ss) positive-sense (+) linear RNA of about 6 kb in size. Virus genome consists of six open reading frames (ORFs) that are expressed by sub-genomic RNAs. The SCYLV is phloem-limited and transmitted by sugarcane aphid Melanaphis sacchari in a circulative and non-propagative manner. The other aphid species namely, Ceratovacuna lanigera, Rhopalosiphum rufiabdominalis, and R. maidis also been reported to transmit the virus. The virus is not transmitted mechanically, therefore, its transmission by M. sacchari has been studied in different countries. SCYLV has a limited natural host range and mainly infect sugarcane (Sachharum hybrid), grain sorghum (Sorghum bicolor), and Columbus grass (Sorghum almum). Recent insights in the protein-protein interactions of Polerovirus through protein interaction reporter (PIR) technology enable us to understand viral encoded proteins during virus replication, assembly, plant defence mechanism, short and long-distance travel of the virus. This review presents the recent understandings on virus biology, diagnosis, genetic diversity, virus-vector and host-virus interactions and conventional and next generation management approaches.

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Section: Next Generation Strategies For Management Of Scylvmentioning

confidence: 99%

Present Status and Future Management Strategies for Sugarcane Yellow Leaf Virus: A Major Constraint to the Global Sugarcane Production

et al. 2020

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“…Nine hundred and ninety-three markers were positioned in the final linkage map and distributed over 223 linkage groups clustered in 18 homologous and homoeologous groups (HGs). You et al [303] used a 100K Affymetrix Axiom Sugarcane SNP array to genotype a full-sib family derived from the Green German and IND81-146 varieties, and a selfing population derived from CP80-1827. The maps obtained revealed higher numbers of markers than previous studies, ranging from 3482 mapped single-dose markers for the Green German parent to 536 for CP80-1827 (see 304 for the comparison).…”

Section: Case Studies 201 Sugarcanementioning

confidence: 99%

Meiosis in Polyploids and Implications for Genetic Mapping: A Review

Soares

Mollinari

Oliveira

et al. 2021

Genes

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Plant cytogenetic studies have provided essential knowledge on chromosome behavior during meiosis, contributing to our understanding of this complex process. In this review, we describe in detail the meiotic process in auto- and allopolyploids from the onset of prophase I through pairing, recombination, and bivalent formation, highlighting recent findings on the genetic control and mode of action of specific proteins that lead to diploid-like meiosis behavior in polyploid species. During the meiosis of newly formed polyploids, related chromosomes (homologous in autopolyploids; homologous and homoeologous in allopolyploids) can combine in complex structures called multivalents. These structures occur when multiple chromosomes simultaneously pair, synapse, and recombine. We discuss the effectiveness of crossover frequency in preventing multivalent formation and favoring regular meiosis. Homoeologous recombination in particular can generate new gene (locus) combinations and phenotypes, but it may destabilize the karyotype and lead to aberrant meiotic behavior, reducing fertility. In crop species, understanding the factors that control pairing and recombination has the potential to provide plant breeders with resources to make fuller use of available chromosome variations in number and structure. We focused on wheat and oilseed rape, since there is an abundance of elucidating studies on this subject, including the molecular characterization of the Ph1 (wheat) and PrBn (oilseed rape) loci, which are known to play a crucial role in regulating meiosis. Finally, we exploited the consequences of chromosome pairing and recombination for genetic map construction in polyploids, highlighting two case studies of complex genomes: (i) modern sugarcane, which has a man-made genome harboring two subgenomes with some recombinant chromosomes; and (ii) hexaploid sweet potato, a naturally occurring polyploid. The recent inclusion of allelic dosage information has improved linkage estimation in polyploids, allowing multilocus genetic maps to be constructed.

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“…Despite the hurdle, several sugarcane genetic maps are based mostly on F 1 progenies from bi-parental crosses (Aitken et al, 2014;Chen et al, 2008;Palhares et al, 2012;Yang et al, 2017) or self-progeny (S 1 ) populations (Andru et al, 2011;Hoarau et al, 2001;You et al, 2019). Andru et al (2011) generated a framework genetic linkage map using an S 1 population derived from LCP 85-384, involving 64 amplified fragment length polymorphism (AFLP), 12 target region amplification polymorphism (TRAP), and 19 simple sequence repeat (SSR) markers.…”

Section: Introductionmentioning

confidence: 99%

“…Unlike other diploid and self‐pollinated species, heterozygous outbred clones are being used to create segregating population for linkage map construction and QTL mapping in sugarcane (Aitken et al., 2014). Despite the hurdle, several sugarcane genetic maps are based mostly on F 1 progenies from bi‐parental crosses (Aitken et al., 2014; Chen et al., 2008; Palhares et al., 2012; Yang et al., 2017) or self‐progeny (S 1 ) populations (Andru et al., 2011; Hoarau et al., 2001; You et al., 2019). Andru et al.…”

Section: Introductionmentioning

confidence: 99%

Identification of quantitative trait loci (QTL) controlling fibre content of sugarcane (Saccharum hybrids spp.)

et al. 2021

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The fibre content (FC) of sugarcane millable stalks is important for both sugar and bioenergy production. Higher FC favours the energy producer while lower FC facilitates the efficient sugar extraction. A molecular marker for FC helps select improved sugarcane cultivars with favourable partitioning of FC for both sugar and energy production industries. A quantitative trait loci (QTL) study was conducted using an enriched linkage map of LCP 85-384 and FC data from two crop cycles (plant cane and first ratoon) of its self-progeny population. A total of five unique QTL were identified across both crop cycles and combined, of which three QTL (qFC020, qFC044 and qFC053) were common explained a total of 22.46%, 23.93% and 25.14% of the phenotypic variances for plant cane, first ratoon and combined data, respectively. As FC values increased gradually, the QTL allele combination effect also increased. Using markers linked to these putative common QTL alleles would benefit the breeders to select sugarcane lines for sugar and bioenergy production.

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Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification

Cited by 44 publications

References 71 publications

Present Status and Future Management Strategies for Sugarcane Yellow Leaf Virus: A Major Constraint to the Global Sugarcane Production

Present Status and Future Management Strategies for Sugarcane Yellow Leaf Virus: A Major Constraint to the Global Sugarcane Production

Meiosis in Polyploids and Implications for Genetic Mapping: A Review

Identification of quantitative trait loci (QTL) controlling fibre content of sugarcane (Saccharum hybrids spp.)

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