A High-Density Genetic Recombination Map of Sequence-Tagged Sites for Sorghum, as a Framework for Comparative Structural and Evolutionary Genomics of Tropical Grains and Grasses

Abstract

We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM (∼300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of ≤50 cM. Significant variations in DNA marker density are related to possible centromeric regions and to probable chromosome structural rearrangements between Sorghum bicolor and S. propinquum, but not to variation in levels of intraspecific allelic richness. While cDNA and genomic clones are similarly distributed across the genome, SSR-containing clones show different abundance patterns. Rapidly evolving hypomethylated DNA may contribute to intraspecific genomic differentiation. Nonrandom distribution patterns of multiple loci detected by 357 probes suggest ancient chromosomal duplication followed by extensive rearrangement and gene loss. Exemplifying the value of these data for comparative genomics, we support and extend prior findings regarding maize-sorghum synteny—in particular, 45% of comparative loci fall outside the inferred colinear/syntenic regions, suggesting that many small rearrangements have occurred since maize-sorghum divergence. These genetically anchored sequence-tagged sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops.

QTLs Associated with Crown Root Angle, Stomatal Conductance, and Maturity in Sorghum

“…After filtering, a total of 6128 SNPs were retained from the initial 282,267 SNP calls that described 2833 recombination bins (Table 2). The length of the map was 1559.9 cM, which is consistent with previously reported high‐density linkage maps of Sorghum bicolor that have lengths spanning from 1059.2 cM to 1713 cM (Menz et al, 2002; Bowers et al, 2003; Mace et al, 2009; Burow et al, 2011; Zou et al, 2012; Zhang et al, 2013; Truong et al, 2014). The high‐density bin map is available in Supplemental File S1.…”

Occurrence of Different Resistance Mechanisms to Acetolactate Synthase Inhibitors in European Sorghum halepense

“…This allotetraploid species (2n = 40) is thought to be derived from naturally occurring hybridization between Sorghum bicolor (L.) Moench and Sorghum propinquum (Kunth) Hichc. (both 2n = 20) followed by chromosome doubling . It is a geophyte, predominantly self-pollinating, a characteristic that would lead to increased homozygosity over time .…”

“…(both 2n = 20) followed by chromosome doubling. 5 It is a geophyte, predominantly selfpollinating, 6 a characteristic that would lead to increased homozygosity over time. 7 It reproduces asexually, via extensive production of rhizomes, which makes it difficult to control, and also sexually by producing a large number of highly dormant seeds.…”

Unraveling the genetic components of perenniality: Toward breeding for perennial grains

“…Because S. propinquum is thought to have been the progenitor that contributed rhizomatousness to S. halepense , comparing the results of this study to those derived from S. bicolor X S. propinquum (Kong et al, 2015; Paterson et al, 1995b) may provide new insight into the evolution of genetic novelty by polyploid S. halepense , facilitating understanding of its competitiveness and aggressiveness. Noting that S. bicolor X S. propinquum interspecific progeny show largely normal transmission genetics, albeit with some segregation distortion and one probable translocation (Bowers et al, 2003), and that S. halepense has proven to be highly durable in nature, meiotic stability and meiotic recombination in these crosses are expected to be largely normal, indeed, with deviations from normality that are interesting potential contributors to mitigation of “escape” (unintended dispersal) of transgenes from transgenic crops.…”