Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations

Abstract

To increase the value of associated molecular tools and also to begin to explore the degree to which interspecific and intraspecific genetic variation in Sorghum is attributable to corresponding genetic loci, we have aligned genetic maps derived from two sorghum populations that share one common parent (Sorghum bicolor L. Moench accession BTx623) but differ in morphological and evolutionarily distant alternate parents (S. propinquum or S. bicolor accession IS3620C). A total of 106 well-distributed DNA markers provide for map alignment, revealing only six nominal differences in marker order that are readily explained by sampling variation or mapping of paralogous loci. We also report a total of 61 new QTLs detected from 17 traits in these crosses. Among eight corresponding traits (some new, some previously published) that could be directly compared between the two maps, QTLs for two (tiller height and tiller number) were found to correspond in a non-random manner (P<0.05). For several other traits, correspondence of subsets of QTLs narrowly missed statistical significance. In particular, several QTLs for leaf senescence were near loci previously mapped for 'stay-green' that have been implicated by others in drought tolerance. These data provide strong validation for the value of molecular tools developed in the interspecific cross for utilization in cultivated sorghum, and begin to separate QTLs that distinguish among Sorghum species from those that are informative within the cultigen (S. bicolor).

3D sorghum reconstructions from depth images identify QTL regulating shoot architecture

“…Because segmentation-dependent traits represent organ-level traits that are often manually measured, QTLs identified via the image-based platform for organ-level traits were compared with QTLs identified previously for similar traits in the BTx623 3 IS3620C population and previous reports on the sorghum dwarfing loci Dw2 and Dw3 (Hart et al, 2001;Feltus et al, 2006;Brown et al, 2008;Mace and Jordan, 2011;Morris et al, 2013;Higgins et al, 2014). Most organlevel QTL intervals found in this study overlap with comparable or related traits from previous field studies (Table II).…”

“…Comparison of QTL intervals identified using image-based phenotyping with previously reported QTL intervals in the literature Most QTL intervals identified with the platform overlapped with QTLs or causal genes reported previously for related phenotypes (Hart et al, 2001;Feltus et al, 2006;Mace and Jordan, 2011;Morris et al, 2013;Higgins et al, 2014). Dw3 was cloned previously (Multani et al, 2003).…”

“…Supplemental Table S1 contains all identified organ-level QTLs. Leaf pitch and leaf curve are both measures of Euclidean distance from the leaf base to the apex of the curved leaf blade and from the leaf base to the leaf tip, respectively (Feltus et al, 2006 (Figs. 4 and 6), a number of improvements will be necessary prior to its applicability in even larger scale studies.…”

“…To compare QTLs found in this study with existing QTLs in the literature, the physical coordinates relative to the sorghum version 1 reference assembly, Sbi1, for QTLs in the BTx623 3 IS3620C population were obtained; Mace and Jordan (2011) determined these physical coordinates using a consensus map and QTLs identified by Hart et al (2001) and Feltus et al (2006). The coordinates of Dw2 and Dw3 were obtained from Morris et al (2013) and Multani et al (2003).…”

A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses

“…We investigated whether our sequenced mutant library could help validate genes located in QTL regions. To this end, we focused on 13 seed size QTL intervals reported in four mapping studies (Paterson et al, 1995;Feltus et al, 2006;Srinivas et al, 2009;Zhang et al, 2015). Four of these 13 genomic regions had been identified in both QTL and GWAS studies.…”