An integrated SSR and RFLP linkage map of <i>Sorghum bicolor</i> (L.) Moench

Abstract

We report the development, testing, and use (for genetic mapping) of a large number of polymerase chain reaction (PCR) primer sets that amplify DNA simple sequence repeat (SSR) loci of Sorghum bicolor (L.) Moench. Most of the primer sets were developed from clones isolated from two sorghum bacterial artificial chromosome (BAC) libraries and three enriched sorghum genomic-DNA (gDNA) libraries. A few were developed from sorghum DNA sequences present in public databases. The libraries were probed with radiolabeled di- and trinucleotide oligomers, the BAC libraries with four and six oligomers, respectively, and the enriched gDNA libraries with four and three oligomers, respectively. Both types of libraries were markedly enriched for SSRs relative to a size-fractionated gDNA library studied earlier. However, only 2% of the sequenced clones obtained from the size-fractionated gDNA library lacked a SSR, whereas 13% and 17% of the sequenced clones obtained from the BAC and enriched gDNA libraries, respectively, lacked a SSR. Primer sets were produced for 313 SSR loci. Two-hundred sixty-six (85%) of the loci were amplified and 165 (53%) of the loci were found to be polymorphic in a population composed of 18 diverse sorghum lines. (AG/TC)n and (AC/TG)n repeats comprised 91% of the dinucleotide SSRs and 52% of all of the SSRs at the polymorphic loci, whereas four types of repeats comprised 66% of the trinucleotide SSRs at the loci. Primer sequences are reported for the 165 polymorphic loci and for eight monomorphic loci that have a high degree of homology to genes. Also reported are the genetic map locations of 113 novel SSR loci (including four SSR-containing gene loci) and a linkage map composed of 147 SSR loci and 323 RFLP (restriction fragment length polymorphism) loci. The number of SSR loci per linkage group ranges from 8 to 30. The SSR loci are distributed relatively evenly throughout approximately 75% of the 1406-cM linkage map, but segments of five linkage groups comprising about 25% of the map either lack or contain few SSR loci. Mapping of SSR loci isolated from BAC clones located to these segments is likely to be the most efficient method for placing SSR loci in the segments.

Construction of a combined sorghum linkage map from two recombinant inbred populations using AFLP, SSR, RFLP, and RAPD markers, and comparison with other sorghum maps

“…Most linkage groups reacted to the parameter settings ("LOD" and "REC" values) with changes in marker order. More stringent parameter settings resulted in erroneous marker orders as judged from the "list of top-linked markers" in the Joinmap output (see Stam and van Ooijen 1995) and compared to the map of Bhattramakki et al (2000). Recombination frequencies were converted to centiMorgans (cM) with Haldane's mapping function (Haldane 1919).…”

“…The "jump" and "triplet" thresholds were set to 4 and 9, respectively. The linkage groups were named according to common SSR markers selected from the map of Bhattramakki et al (2000).…”

“…The RIPs were then genotyped with one to three anchor RFLP markers per linkage group. SSR analyses were done by Celera AgGen (Davis, Calif., USA) using microsatellites developed by Brown et al (1996), Taramino et al (1997), Kong et al (2000) and Bhattramakki et al (2000). PCR conditions were standard, following the recommendations of the aforementioned authors.…”

“…A number of genetic linkage maps of sorghum have been published in the last decade (see Table 1). Several are purely based on RFLP (restriction fragment length polymorphism) markers (Hulbert et al 1990;Binelli et al 1992;Whitkus et al 1992;Berhan et al 1993;Chittenden et al 1994;Pereira et al 1994;Ragab et al 1994;Xu et al 1994;Dufour et al 1997;Ming et al 1998;Crasta et al 1999;Peng et al 1999;Bowers et al 2000;Xu et al 2000); others include also AFLP (amplified fragment length polymorphism; Boivin et al 1999;Klein et al 2001), SSR (simple-sequence repeats; Taramino et al 1997;Tao et al 1998Tao et al , 2000Bhattramakki et al 2000;Kong et al 2000;Bennetzen et al 2001;Klein et al 2001), RAPD (randomly amplified polymorphic DNA; Tuinstra et al 1996Tuinstra et al , 1997, or morphological markers (Bennetzen et al 2001). But all of these genetic maps still have deficiencies, including the absence of mapped telomeres and centromeres, and a lack of connections to the physical chromosomal structures.…”

Detection of quantitative trait loci (qtl) associated with yield and yield component traits in sorghum [Sorghum bicolor (L.) Moench] sown early and late planting dates

“…A genetic linkage map consisting 11 linkage groups was constructed in which chromosome A was found to be broken into two linkage groups according to Bhattramakki et al (2000). We used SSR markers from this published map to anchor the relatively new DArT markers.…”