Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae)

Abstract

BackgroundDomestication has played an important role in shaping characteristics of the inflorescence and plant height in cultivated cereals. Taking advantage of meta-analysis of QTLs, phylogenetic analyses in 502 diverse sorghum accessions, GWAS in a sorghum association panel (n = 354) and comparative data, we provide insight into the genetic basis of the domestication traits in sorghum and rice.ResultsWe performed genome-wide association studies (GWAS) on 6 traits related to inflorescence morphology and 6 traits related to plant height in sorghum, comparing the genomic regions implicated in these traits by GWAS and QTL mapping, respectively. In a search for signatures of selection, we identify genomic regions that may contribute to sorghum domestication regarding plant height, flowering time and pericarp color. Comparative studies across taxa show functionally conserved ‘hotspots’ in sorghum and rice for awn presence and pericarp color that do not appear to reflect corresponding single genes but may indicate co-regulated clusters of genes. We also reveal homoeologous regions retaining similar functions for plant height and flowering time since genome duplication an estimated 70 million years ago or more in a common ancestor of cereals. In most such homoeologous QTL pairs, only one QTL interval exhibits strong selection signals in modern sorghum.ConclusionsIntersections among QTL, GWAS and comparative data advance knowledge of genetic determinants of inflorescence and plant height components in sorghum, and add new dimensions to comparisons between sorghum and rice.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0477-6) contains supplementary material, which is available to authorized users.

A High-Throughput, Field-Based Phenotyping Technology for Tall Biomass Crops

“…Dw2 has been mapped to chromosome 6 (Feltus et al, 2006;Zou et al, 2012;Nagaraja Reddy et al, 2013), and its effect on plant height is frequently detected in GWAS as a large genomic region encompassing almost the entire chromosome 6. This particular result is the consequence of the genetically converted sorghum accessions included in diversity panels such as the one investigated here (Klein et al, 2008;Morris et al, 2013;Zhang et al, 2015). Several linkage disequilibrium and linkage mapping studies also confirmed the location, importance, and effects of these two regions on chromosomes 6 and 9 on plant height (Upadhyaya et al, 2012;Zou et al, 2012;Morris et al, 2013, Nagaraja Reddy et al, 2013Zhang et al, 2015;Zhao et al, 2016).…”

“…This particular result is the consequence of the genetically converted sorghum accessions included in diversity panels such as the one investigated here (Klein et al, 2008;Morris et al, 2013;Zhang et al, 2015). Several linkage disequilibrium and linkage mapping studies also confirmed the location, importance, and effects of these two regions on chromosomes 6 and 9 on plant height (Upadhyaya et al, 2012;Zou et al, 2012;Morris et al, 2013, Nagaraja Reddy et al, 2013Zhang et al, 2015;Zhao et al, 2016). In spite of the similar performance and efficiency of both algorithms to estimate the actual morphological trait, Auto-PHe has the advantage of being an automatic processing pipeline with reduced run time and concomitant cost.…”

Genome‐Wide Association Study for Nine Plant Architecture Traits in Sorghum

“…In sorghum, a few association mapping studies have been performed to investigate specific plant characteristics using a diversity panel (Brown et al, 2008; Shehzad et al, 2009; Murray et al, 2009; Mantilla Perez et al, 2014) and a mini core panel (Upadhyaya et al, 2012a,b) with limited genome coverage. Additionally, several GWAS have been recently conducted using high‐throughput genotyping data to discover the genetic control of grain polyphenol concentration (Rhodes et al, 2014), flavonoid pigmentation traits (Morris et al, 2013b), aluminum tolerance and grain yield in P‐limited environments (Leiser et al, 2014), resistance to stalk rot diseases (Adeyanju et al, 2015), seed size (Zhang et al, 2015b), and plant height and inflorescence trait components (Morris et al, 2013a; Zhang et al, 2015a).…”

Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L

“…Genome-wide association study (GWAS) with SNPs generated by genotyping by sequencing (GBS) has been widely used in all major crops including maize, rice, barley, tomato, wheat, sorghum, soybean, watermelon and several other important plant species1011121314 and found effective for mining new genes; however, the population structure must be resolved accurately to reduce spurious associations because of confounding effects of subpopulations. The current research aims to identify genomic segments linked to various fruit traits and capsaicin accumulation in diverse collections of C. annuum .…”