Genetic analysis of the sugarcane (Saccharum spp.) cultivar ‘LCP 85-384’. I. Linkage mapping using AFLP, SSR, and TRAP markers

Abstract

Sugarcane hybrids are complex aneu-polyploids (2n = 100-130) derived from inter-specific hybridization between ancestral polyploid species, namely S. officinarum L. and S. spontaneum L. Efforts to understand the sugarcane genome have recently been enhanced through the use of new molecular marker technologies. A framework genetic linkage map of Louisiana's popular cultivar LCP 85-384 was constructed using the selfed progeny and based on polymorphism derived from 64 AFLP, 19 SSR and 12 TRAP primer pairs. Of 1,111 polymorphic markers detected, 773 simplex (segregated in 3:1 ratio) and 182 duplex (segregate in 77:4 ratio) markers were used to construct the map using a LOD value of ≥ 4.0 and recombination threshold of 0.44. The genetic distances between pairs of markers linked in the coupling phase was computed using the Kosambi mapping function. Of the 955 markers, 718 simplex and 66 duplex markers were assigned to 108 co-segregation groups (CGs) with a cumulative map length of 5,617 cM and a density of 7.16 cM per marker. Fifty-five simplex and 116 duplex markers remained unlinked. With an estimated genome size of 12,313 cM for LCP 85-384, the map covered approximately 45.6% of the genome. Forty-four of the 108 CGs were assigned into 9 homo(eo)logous groups (HGs) based on information from locus-specific SSR and duplex markers, and repulsion phase linkages detected between CGs. Meiotic behavior of chromosomes in cytogenetic studies and repulsion phase linkage analysis between CGs in this study inferred the existence of strong preferential chromosome pairing behavior in LCP 85-384. This framework map marks an important beginning for future mapping of QTLs associated with important agronomic traits in the Louisiana sugarcane breeding programs.

Agromorphological characterization of Sesamum radiatum (Schum. and Thonn.), a neglected and underutilized species of traditional leafy vegetable of great importance in Benin)

“…accessions, the use of molecular markers such as AFLPs (Andru et al, 2011) will be necessary as it was the case for many crops such as fonio (Adoukonou et al, 2007), wheat (Altintas et al, 2008), yam (Sonibare et al, 2010) and rice (Rajkumar et al, 2011).…”

Genetic Diversity Analysis of Sugarcane Germplasm Based on Fluorescence-Labeled Simple Sequence Repeat Markers and a Capillary Electrophoresis-based Genotyping Platform

“…However, phenotypic traits usually do not reflect the true level of diversity among sugarcane germplasm due to severe influence by environmental factors (Creste et al 2010;Singh et al 2010). To obtain reliable data to distinguish the genetic diversity among breeding lines in programs, DNA markers have also been used, including AFLP (amplified fragment length polymorphism) (Aitken et al 2006;Besse et al 1998), RFLP (restriction fragment length polymorphism) (Creste et al 2010), RAPD (random amplification polymorphism DNA) (Da Nawaz et al 2010;Ramakrishnan et al 2015), SRAP (sequence-related amplified polymorphism) (Alwala et al 2008;Chang et al 2012), SCoT (start codon targeted) (Que et al 2014), SSR (simple sequence repeat) Andru et al 2011;Cai et al 2005;Nayak et al 2014;Xu et al 1999;Zawedde et al 2014), ISSR (inter simple sequence repeat) (Alves de Almeida et al 2009;Devarumath et al 2012), and EST (expressed sequences tags)-SSR Singh et al 2013). Among these markers, SSR markers are highly informative, simple to use with reliable results (Senior et al 1998;Smith et al 1997), and have been widely applied to sugarcane Pan 2010;Pan et al 2003).…”

Sugarcane Genetics and Genomics

“…LCP 85-384 chromosomes confirmed the high incidence of bivalent pairing among homologous chromosomes in this hybrid. Repulsion phase linkages found among three or more markers in some linkage groups are suggestive of disomic inheritance or preferential pairing of chromosomes in LCP 85-384 (Andru et al 2011).…”

“…A linkage map was constructed with 1,111 AFLP, SSR, and TRAP markers, and 108 linkage groups were assigned into nine HGs (Andru et al 2011).…”