Progress and Prospects of Association Mapping in Sugarcane (Saccharum Species Hybrid), a Complex Polyploid Crop

Banerjee, Nandita; Khan, Mohammad Suhail; Swapna, M.; Singh, Rameshwar; Kumar, Sanjeev

doi:10.1007/s12355-020-00852-9

Cited by 14 publications

(5 citation statements)

References 80 publications

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“…Association mapping is also conducted for hybrids of many plant species [94][95][96][97]. Recently, an attempt has been made to study the relationship between molecular markers and heterosis effects in maize [33].…”

Section: Discussionmentioning

confidence: 99%

Meta-Analysis of Influence of Diversity of Parental Forms on Heterosis and Specific Combining Ability of Their Hybrids

2023

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An important stage in any breeding activity is selection of suitable individuals for further breeding. Thus, the main goal of breeders becomes such a selection of parental forms that leads to the consolidation and maximization of the value of traits of significant utility and economic importance. Heterosis and specific combining ability are very important parameters in plant and animal breeding. The ability to predict their value and relevance could significantly shorten the breeding process. One way to predict the effects of heterosis and specific combining ability is to select parental forms for crosses. This selection can be made on the basis of variation in parental forms. An analysis was made of publicly available data that contain information about the effects of heterosis, the effects of specific combining ability, and phenotypic and genetic diversity of parental forms. Preliminary studies show that the best approach for obtaining favorable hybrids would be selection of parental forms that are very genetically diverse while being phenotypically equal.

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Section: Discussionmentioning

confidence: 99%

Meta-Analysis of Influence of Diversity of Parental Forms on Heterosis and Specific Combining Ability of Their Hybrids

2023

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“…To increase sugarcane production in a sustainable way, breeding new sugarcane varieties for higher yield is essential ( Yang et al, 2020 ). However, sugarcane has one of the most complex genomes of all crop plants due to its high ploidy level, high heterozygosity, frequent aneuploidy, and large genome size (approximately 10 Gb) ( Banerjee et al, 2020 ; Grivet & Arruda, 2002 ; Mancini et al, 2017 ; Thirugnanasambandam, Hoang & Henry, 2018 ). Modern sugarcane cultivars (2n = 100−140) were derived from interspecific crosses between S. officinarum (2n = 8x = 80; x = 10) and S. spontaneum (2n = 5x − 16x = 40 − 128; x = 8), followed by several backcrosses with S. officinarum , contributing about 80% and 10–20% to the hybrid genome, respectively ( D’Hont et al, 1998 ; D’Hont, 2005 ; Grivet & Arruda, 2002 ; Shearman et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

A SNP variation in the Sucrose synthase (SoSUS) gene associated with sugar-related traits in sugarcane

Khanbo,

Somyong,

Phetchawang

et al. 2023

PeerJ

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Background Sugarcane (Saccharum spp.) is an economically significant crop for both the sugar and biofuel industries. Breeding sugarcane cultivars with high-performance agronomic traits is the most effective approach for meeting the rising demand for sugar and biofuels. Molecular markers associated with relevant agronomic traits could drastically reduce the time and resources required to develop new sugarcane varieties. Previous sugarcane candidate gene association analyses have found single nucleotide polymorphism (SNP) markers associated with sugar-related traits. This study aims to validate these associated SNP markers of six genes, including Lesion simulating disease 1 (LSD), Calreticulin (CALR), Sucrose synthase 1 (SUS1), DEAD-box ATP-dependent RNA helicase (RH), KANADI1 (KAN1), and Sodium/hydrogen exchanger 7 (NHX7), in a diverse population in 2-year and two-location evaluations. Methods After genotyping of seven targeted SNP markers was performed by PCR Allelic Competitive Extension (PACE) SNP genotyping, the association with sugar-related traits and important cane yield component traits was determined on a set of 159 sugarcane genotypes. The marker-trait relationships were validated and identified by both t-test analysis and an association analysis based on the general linear model. Results The mSoSUS1_SNPCh10.T/C and mSoKAN1_SNPCh7.T/C markers that were designed from the SUS1 and KAN1 genes, respectively, showed significant associations with different amounts of sugar-related traits and yield components. The mSoSUS1_SNPCh10.T/C marker was found to have more significant association with sugar-related traits, including pol, CCS, brix, fiber and sugar yield, with p values of 6.08 × 10−6 to 4.35 × 10−2, as well as some cane yield component traits with p values of 1.61 × 10−4 to 3.35 × 10−2. The significant association is consistent across four environments. Conclusion Sucrose synthase (SUS) is considered a crucial enzyme involved in sucrose metabolism. This marker is a high potential functional marker that may be used in sugarcane breeding programs to select superior sugarcane with good fiber and high sugar contents.

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“…Other studies have also reported GWAS investigations on the identification of genetic loci for disease resistance, 29−31 leaf angle, 32 and economic traits 33−41 in sugar cane. However, most of the current GWAS analyses in sugar cane have primarily been conducted on the species S. officinarum and S. spontaneum, as well as modern varieties/genotypes that encompass the genomes of these two previous Saccharum species, 42 and only a limited number of studies have focused on hybrid progeny derived from Saccharum-related genera that possess potential in sugar cane breeding programs, such as Miscanthus 43 and Erianthus. 44 To broaden the genetic background of sugar cane, we generated a population consisting of 159 offsprings that originated from the cross of T. arundinaceum 87-36 (2n = 60) with S. spontaneum 79-9 (2n = 64), as well as the backcross with commercial variety in our previous work.…”

Section: ■ Introductionmentioning

confidence: 99%

“…officinarum and S. spontaneum, as well as modern varieties/genotypes that encompass the genomes of these two previous Saccharum species, and only a limited number of studies have focused on hybrid progeny derived from Saccharum-related genera that possess potential in sugar cane breeding programs, such as Miscanthus and Erianthus …”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane

Zhang,

Huang,

Zhang

et al. 2023

J. Agric. Food Chem.

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Sugarcane, a major sugar and energy crop worldwide faces an increasing demand for higher yields. Identifying yieldrelated markers and candidate genes is valuable for breeding high-yield varieties using molecular techniques. In this work, seven yield-related traits were evaluated in a diversity panel of 159 genotypes, derived from Tripidium arundinaceum, Saccharum spontaneum, and modern sugarcane genotypes. All traits exhibited significant genetic variance with high heritability and high correlations. Genetic diversity analysis reveals a genomic decay of 23 kb and an average single nucleotide polymorphism (SNP) number of 25,429 per genotype. These 159 genotypes were divided into 4 subgroups. Genome-wide association analysis identified 47 SNPs associated with brix, spanning 36 quantitative trait loci (QTLs), and 138 SNPs for other traits across 104 QTLs, covering all 32 chromosomes. Interestingly, 12 stable QTLs associated with yield-related traits were identified, which contained 35 candidate genes. This work provides markers and candidate genes for marker-assisted breeding to improve sugarcane yields.

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Progress and Prospects of Association Mapping in Sugarcane (Saccharum Species Hybrid), a Complex Polyploid Crop

Cited by 14 publications

References 80 publications

Meta-Analysis of Influence of Diversity of Parental Forms on Heterosis and Specific Combining Ability of Their Hybrids

Meta-Analysis of Influence of Diversity of Parental Forms on Heterosis and Specific Combining Ability of Their Hybrids

A SNP variation in the Sucrose synthase (SoSUS) gene associated with sugar-related traits in sugarcane

Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane

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