Genome-wide association study of multiple yield components in a diversity panel of polyploid sugarcane (Saccharum spp.)

Abstract

25Sugarcane (Saccharum spp.) is an important economic crop, contributes up to 80% of 26 sugar and approximately 60% bio-fuel globally. To meet the increased demand for sugar and 27 bio-fuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield 28 components. Therefore, dissection of causal DNA sequence variants is of great importance by 29 providing genetic resources and fundamental information for crop improvement. In this study, 30 we evaluated and analyzed nine yield components in a sugarcane diversity panel consisting of 31 308 accessions primarily selected from the "world collection of sugarcane and related grasses". 32 By genotyping the diversity panel using target enrichment sequencing, we identified a large 33 number of sequence variants. Genome-wide association study between the markers and traits 34 were conducted with dosages and gene actions taken into consideration. In total, 217 non-35 redundant markers and 225 candidate genes were identified to be significantly associated with 36 the yield components, which can serve as a comprehensive genetic resource database for future 37 gene identification, characterization, and selection for sugarcane improvement. We further 38 investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 39 ROHs, and found that the occurrence of ROH in the genome were non-random and probably 40 under selection. ROHs were associated with total weight and dry weight, and high ROHs 41 resulted in decrease of the two traits. This study approved that genomic inbreeding has led to 42 negative impacts on sugarcane yield. 43 GWAS 45 46As an important cash crop, sugarcane (Saccharum spp.) contributes up to 80% of sugar 48 and approximately 60% bio-fuel globally (Dahlquist 2013). To meet the increasing global 49 demand for sugar and bio-fuel, sugarcane harvest area in the world has increased from 22.7 to 50 26.8 million hectares in the last ten years (FAO 2016). However, cropping areas for sugarcane 51 could not be increased indefinitely due to the limited farming land areas and competition with 52 food crops. In order to sustainably improve sugarcane production, breeding sugarcane cultivars 53 with high performance for yield components is critical. Thus, evaluating yield components in 54 sugarcane germplasm and dissecting the genetic basis of causal sequence variants are of great 55 importance to fulfill this strategy by providing tools and genetic resources. 56 The Saccharum genus consists of two wild species (S. spontaneum and S. robustum) 57 and four cultivated species (S. officinarum, S. barberi, S. sinence, and S. edule) (Daniels and 58 Roach 1987). All the Saccharum species are readily intercrossed except sterile S. edule. Modern 59 sugarcane hybrids were primarily derived from inter-species hybridization between S. 60 spontaneum (2n = 40-128, x = 8) and S. officinarum (2n = 80, x = 10) followed by several 61 backcrosses with S. officinarum. Therefore, modern sugarcane hybrids have a chromoso...

Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance

“…Because we would not need to calculate chromosomal distances between loci for linkage map construction, the elevated loss of markers and the reduced performance of ADs in the task of genomic prediction, we decided to continue our analyses with APs. Previous tests of this approach yielded reasonable results 101,102,104 .…”

“…Song et al 100 , for example, designed different probes using in silico approaches. The resulting regions were posteriorly adopted in other studies [101][102][103][104] due to the large quantity of markers with sufficient sequencing depth located in genic regions. Another approach is GBS 5, 23, 28, 105-107 , which is the preferred genotyping method for plants with some degree of genomic complexity 23, 108 mainly due to its simplicity, reproducibility and considerable genome coverage 109 .…”

“…Sequencing reads are generally organized by using the S. bicolor genome for comparative alignments and the subsequent identification of putative variants with bioinformatic methods. This reference choice is due to sorghum's phylogenetic proximity to sugarcane 5, 28, 105-107 and, in some cases, probe experimental design [100][101][102][103][104] . Despite sorghum's genome usage, the availability of sugarcane pseudoreferences has provided new genomic tools for scientific research as initially explored by Balsalobre et al 23 , who used the sorghum genome, a sugarcane MF genome 65 , a sugarcane leaf transcriptome 51 and SUCEST tags 68 .…”

Molecular diversity and genetic structure of Saccharum complex accessions

“…Thereby, when we analyzed the second PCA (Fig 1B), the close position between breeding accessions and some representatives of S. officinarum (for example, AJAX, CAIANA RIS-CADA, CAYANA, NG21-21, NG57-221, SAC OFFIC 8272 and WHITE MAURITIUS) became more evident and could be explained by the fact that this specie was one of the main ancestors of modern sugarcane cultivars, which carry 80-85% of the S. officinarum genetic base [15]. Furthermore, the evolutionary history of sugarcane may be inferred in the clustering of the second PCA for the A group, since the S. barberi accessions (AGOULE, CHIN, CHUNNE, GANDA CHENI and WHITE PARARIA) were close positioned with some S. officinarum accessions (CAIANA RISCADA, CAIANA VERDADEIRA, CANA BLANCA, IN84-103, NG21-17, SAC OFFIC 8272, SAC OFFIC 8276, SAC OFFIC 8280 and WHITE MAURITIUS) and some S. spontaneum accessions (KRAKATAU and SES205A), possibly because S. barberi were originated from the hybridization of S. officinarum with S. spontaneum [17,18,[84][85][86]. The relatedness of modern sugarcane cultivars also appears to be represented in the second PCA, since some FH accessions (NA56-79, POJ2878, TUC71-7, Co290, Co331, Co413 and Co419) used as parents in crosses to obtain Brazilian cultivars were close positioned of BB accessions, for example, the FH accession TUC71-7 was near to their progenies RB855453, RB855574 and RB855196.…”

“…However, the STRUCTURE results should be viewed with caution, since it is based on the assumption that all loci are considered to be in Hardy-Weinberg equilibrium within each population, without any linkage disequilibrium among loci, if they are not closely linked [87]. Thus, for complex genomes such as sugarcane, these assumptions are not fulfilled, even more when are used nonneutral markers related with traits under selection during generations [24,86,88]. Nevertheless, the comparison between PCA, STRUCTURE results and also phylogenetic tree (Fig 2), showed a good way to infer the genetic structure for BPSG.…”