Linkage mapping and genome analysis in a Saccharum interspecific cross using AFLP, SRAP and TRAP markers

Alwala, Sreedhar; Kimbeng, C. A.; Veremis, J. C.; Gravois, K. A.

doi:10.1007/s10681-007-9634-9

Cited by 53 publications

(35 citation statements)

References 51 publications

(106 reference statements)

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“…Marker names with 'EM' or 'PM' represent EcoRI-MseI and PstI-MseI based AFLP markers, respectively, 'sr' represent SRAP markers and 'sus', 'cd' or 'sai' represent TRAP markers. The asterisk indicates markers aVected by segregation distortion (see Alwala et al 2008b …”

Section: Discussionmentioning

confidence: 99%

“…The framework map of S. oYcinarum comprised of 146 linked markers spread over 49 linkage groups while the S. spontaneum map comprised of 121 linked markers in 45 linkage groups. A detailed mapping study has been previously reported (Alwala et al 2008b). …”

Section: Genotyping and Linkage Map Constructionmentioning

confidence: 99%

“…adj. R 2 = 37.9 a The construction of linkage groups was described in Alwala et al (2008b) b Markers that were repeated across seasons and crop-years are denoted in either bold, italics or underlined. Marker names starting with 'EM' or 'PM' represent EcoRI-MseI and PstI-MseI based AFLP markers, respectively, 'sr' represent SRAP markers while 'sus' represent TRAP markers c The threshold LOD score was 3.01 as detected by 1,000 run permutation tests and the QTLs with >3.01 LOD score in any one season or crop-year were declared putative QTLs d Partial R 2 is the proportion of phenotypic variation explained by individual QTLs and adjusted R 2 is the proportion of total phenotypic variation explained by all QTLs in the Wnal model after adjusting for number of terms in the multiple regression model explaining a variation of 7.0% and 4.8%, respectively.…”

Section: Saccharum Spontaneummentioning

confidence: 99%

“…The notion that TRAP, SRAP and PstI-MseI-AFLP primers could be targeting gene rich regions of the genome has made them attractive tools for QTL mapping studies (Li and Quiros 2001;Liu et al 2005;Wang et al 2006;Miklas et al 2006;Alwala et al 2006Alwala et al , 2008b and prompted us to include them in our study. Sequenced SRAP amplicons from Brassica (Li and Quiros 2001) and Cucurbita (Ferriol et al 2003) when used in BLAST searches revealed signiWcant similarities to reported gene sequences found in Genebank databases.…”

Section: L49mentioning

confidence: 99%

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Identification of molecular markers associated with sugar-related traits in a Saccharum interspecific cross

et al. 2009

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The cultivated sugarcane (Saccharum spp. hybrids, 2n = 100-130) is one crop for which interspeciWc hybridization involving wild germplasm has provided a major breakthrough in its improvement. Few clones were used in the initial hybridization event leading to a narrow genetic base for continued cultivar development. Molecular breeding would facilitate the identiWcation and introgression of novel alleles/genes from the wild germplasm into cultivated sugarcane. We report the identiWcation of molecular markers associated with sugar-related traits using an F 1 population derived from a cross between S. oYcinarum 'Louisiana Striped' £ S. spontaneum 'SES 147B', the two major progenitor species of cultivated sugarcane. Genetic linkage maps of the S. oYcinarum and S. spontaneum parents were produced using the AFLP, SRAP and TRAP molecular marker techniques. The mapping population was evaluated for sugar-related traits namely, Brix (B) and pol (P) at the early (E) and late (L) plant growing season in the plant cane (04) and Wrst ratoon (05) crops (04EB, 04LB, 04LP, 05EB and 05EP). For S. oYcinarum, combined across all the traits, a total of 30 putative QTLs was observed with LOD scores ranging from 2.51 to 7.48. The phenotypic variation (adj. R 2 ) explained by all QTLs per trait ranged from 22.1% (04LP) to 48.4% (04EB). For S. spontaneum, a total of 11 putative QTLs was observed with LOD scores ranging from 2.62 to 4.70 and adj. R 2 ranging from 9.3% (04LP) to 43.0% (04LB). Nine digenic interactions (iQTL) were observed in S. oYcinarum whereas only three were observed in S. spontaneum. About half of the QTLs contributed by both progenitor species were associated with eVects on the trait that was contrary to expectations based on the phenotype of the parent contributing the allele. Quantitative trait loci and their associated eVects were consistent across crop-years and growing seasons with very few QTLs being unique to the early season. When the data were reanalyzed using the non-parametric discriminant analysis (DA) approach, signiWcant marker-trait associations were detected for markers that were either identical to or in the vicinity of markers previously identiWed using the traditional QTL approach. Discriminant analysis also pointed to previously

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Section: Discussionmentioning

confidence: 99%

Section: Genotyping and Linkage Map Constructionmentioning

confidence: 99%

Section: Saccharum Spontaneummentioning

confidence: 99%

Section: L49mentioning

confidence: 99%

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Identification of molecular markers associated with sugar-related traits in a Saccharum interspecific cross

et al. 2009

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“…Conversely, studies of progeny derived from the S. spontaneum clones cv. SES 208 (Al-Janabi et al 1993;da Silva et al 1993), IND 81-146 (Edmé et al 2005), and SES 147B (Alwala et al 2008) resulted in the construction of linkage maps showing a general lack of a repulsion phase, which suggests that these S. spontaneum clones are autopolyploids undergoing random chromosome pairing. The RFLP study of 282 F 2 progeny of sugarcane hybrid R570 showed the two ancestral species differed over a continuous range of paring affinity, which may reflect an unsystematic meiotic behavior of complex polyploids such as sugarcane hybrids (Jannoo et al 2004).…”

Section: Molecular Cytogeneticsmentioning

confidence: 99%

Sugarcane Genetics and Genomics

Zhang

Zhou

Walsh

et al. 2013

Sugarcane: Physiology, Biochemistry, and Functional Biology

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Five decades of productivity gains in the Louisiana sugar industry

Blanchard,

Taylor,

Pontif

et al. 2023

Crop Science

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This study analyzed trends across five decades of productivity data from the Louisiana Sugar Industry, from 1969 to 2021, for sucrose content, cane yield, and sugar yield. Trends over the five decades were revealed using robust regression models, and the least square means allowed for decade‐wise comparisons of trends. Sucrose content increased 45%, from 80.9 ± 6.4 g kg−1 in the first (1969‐1979) to 116.7 ± 4.8 g kg−1 in the fifth (2010‐2021) decade, at 0.85 ± 0.06 g kg−1 per year. Cane yield increased slower (32.2%), from 57.7 ± 5.9 Mg ha −1 in the first to 76.3 ± 6.3 Mg ha−1 in the fifth decade, at 0.45 ± 0.07 Mg ha−1 per year. Sugar yield increased 93% from the first (4.6 ± Mg ha−1) to the fifth (8.9 ± 0.76 Mg ha−1) decade at 0.1 ± 0.01 Mg ha−1 per year. The gains were neither significant nor consistent when comparing successive decades, incremental rather than rapid, and maintained once achieved. Significant (p < 0.05) gains in all traits occurred only in the third decade (1990‐1999) with yearly increases of 1.15 ± 0.30 g kg−1 for sucrose content, 3.00 ± 0.27 Mg ha −1 for cane yield, and 0.35 ± 0.05 Mg ha−1 for sugar yield. Comparisons of trait means between successive decades found both significant (p < 0.05) and non‐significant (p > 0.05) differences, however, comparisons between non‐contiguous decades were all significant (p < 0.05). Variety development accounted for 60% of the progress with sucrose content contributing more (10% more) compared with cane yield. The Louisiana sugar industry has experienced substantial productivity gains in the last five decades thanks to a combination of factors with variety development being the most impactful.This article is protected by copyright. All rights reserved

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Linkage mapping and genome analysis in a Saccharum interspecific cross using AFLP, SRAP and TRAP markers

Cited by 53 publications

References 51 publications

Identification of molecular markers associated with sugar-related traits in a Saccharum interspecific cross

Identification of molecular markers associated with sugar-related traits in a Saccharum interspecific cross

Sugarcane Genetics and Genomics

Five decades of productivity gains in the Louisiana sugar industry

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