A major QTL and an SSR marker associated with glycoalkaloid content in potato tubers from Solanum tuberosum × S. sparsipilum located on chromosome I

Abstract

New potato (Solanum tuberosum) varieties are required to contain low levels of the toxic glycoalkaloids and a potential approach to obtain this is through marker-assisted selection (MAS). Before applying MAS it is necessary to map quantitative trait loci (QTLs) for glycoalkaloid content in potato tubers and identify markers that link tightly to this trait. In this study, tubers of a dihaploid BC(1) population, originating from a cross between 90-HAF-01 (S. tuberosum(1)) and 90-HAG-15 (S. tuberosum(2) x S. sparsipilum), were evaluated for content of alpha-solanine and alpha-chaconine (total glycoalkaloid, TGA) after field trials. In addition, tubers were assayed for TGA content after exposure to light. A detailed analysis of segregation patterns indicated that a major QTL is responsible for the TGA content in tubers of this potato population. One highly significant QTL was mapped to chromosome I of the HAG and the HAF parent. Quantitative trait loci for glycoalkaloid production in foliage of different Solanum species have previously been mapped to this chromosome. In the present research, QTLs for alpha-solanine and alpha-chaconine content were mapped to the same location as for TGA content. Similar results were observed for tubers exposed to light. The simple sequence repeat marker STM5136 was closely linked to the identified QTL.

Development and application of a 20K SNP array in potato

“…This SNP is located at 160kb distance from GAME9 (Cárdenas et al 2016) suggesting linkage disequilibrium between a SNP and a GAME9 allele increasing SGA contents. The QTL Sga1.1 was validated in the SH × RH population, and also co-localizes with the QTL identified by Sørensen et al (2008). In our study Sga1.1 is the QTL with the largest effect, which confirms the characterisation of GAME9 as a key regulator of the SGA pathway (Cárdenas et al 2016).…”

“…While most studies measure SGA levels in potato leaves (Manrique-Carpintero et al 2013;Manrique-Carpintero et al 2014;Medina et al 2002;Ronning et al 1999;Sagredo et al 2006;Sagredo et al 2011;Yencho et al 1998), a few have also been conducted on SGA accumulation in tubers (Mariot et al 2016;Sørensen et al 2008;Valcarcel et al 2014). The majority of these mapping studies involved hybrids with wild species like S. sparsipilum (Sørensen et al 2008) S. berthaulthii (Yencho et al 1998), S. phureja (Medina et al 2002), S. commersonii (Carputo et al 2003) and S. chacoense (Manrique-Carpintero et al 2014;Medina et al 2002;Ronning et al 1999;Sagredo et al 2006;Sagredo et al 2011). This suggests the involvement of alleles originating from wild species in the accumulation of SGA content in the contemporary potato germplasm.…”

“…This suggests the involvement of alleles originating from wild species in the accumulation of SGA content in the contemporary potato germplasm. Six mapping studies reported a QTL for accumulation of SGAs on chromosome 1 (Hutvágner et al 2001;ManriqueCarpintero et al 2014;Ronning et al 1999;Sagredo et al 2011;Sørensen et al 2008;Yencho et al 1998). Additionally, α-solanine and α-chaconine QTLs have been mapped on chromosomes 6 and 11 in two studies (Manrique-Carpintero et al 2014;Yencho et al 1998) and on chromosomes 4, 8 and 12 (Yencho et al 1998){Yencho, 1998Yencho, 1998 #55}.…”

“…Additionally, α-solanine and α-chaconine QTLs have been mapped on chromosomes 6 and 11 in two studies (Manrique-Carpintero et al 2014;Yencho et al 1998) and on chromosomes 4, 8 and 12 (Yencho et al 1998){Yencho, 1998Yencho, 1998 #55}. However, the only QTL found for accumulation of α-solanine and α-chaconine in tubers is on chromosome 1 (Sørensen et al 2008). The major genes involved in the SGA biosynthetic pathway in Solanaceae have recently been published (Itkin et al 2013).…”

“…It has been shown that SGT-genes are responsible for the final glycosylation steps in the SGA pathway (McCue et al 2011;McCue et al 2005;Moehs et al 1997). In the paper of Cárdenas et al (2016) GAME9 was postulated as a major regulator of the SGA pathway which co-localized with the QTL on chromosome 1 from Sørensen et al (2008). From these studies the key-metabolic and regulator genes of the SGA pathway are known, however to be able to apply this knowledge to marker assisted selection in a breeding program, it is essential to know which allelic variants of these genes are responsible for variation in SGA content in potato tubers.…”