Genomic Analysis of a Sorghum NAM Population: High Resolution Mapping of Flowering Time and Plant Height Sophie Bouchet, Marcus O. Olatoye, Sandeep Marla, Brian Wempe, Ram Perumal, Tesfaye Tesso, Mitch Tuinstra#, Jianming Yu*, Geoffrey P. Morris. Email:
[email protected],
[email protected]
Department of Agronomy, Kansas State University, Manha8an KS. #Purdue University, West LafayeLe IN. *Iowa State University, Ames IA.
IntroducQon
Material and Method v Ten founders covering sorghum diversity were crossed to the common parent Tx430 (Table. 1). Recombinant inbred lines (RILs) were derived by single seed descent for 7 generaQons without selecQon (Fig. 1). v In total, 2400 RILs were genotyped with genotyping-‐by-‐sequencing markers using ApeKI restricQon enzyme. Reads were counted and populated using Tassel pipeline [2]. Preliminary analyses were done using 100 000 markers that were polymorphic in at least one family. Missing data were imputed with Beagle [3]. v The NAM populaQon was evaluated in two locaQons (one semi-‐arid in Western Kansas and one humid conQnental in Eastern Kansas) for flowering Qme (FT) and plant height (PTHT). v GWAS were implemented with GCTA [15], QTL mapping with r-‐QTL [16].
Name PI Origin GeneGc structure Traits RTx430 PI655996 Texas A&M G=0.5 ; C=0.3 Breeding line Ajabsido PI656015 Sudan C=0.7 ; D=0.2 ; G=0.1 Macia PI565121 Zimbabwe C=1 P898012 PI656057 India C=1 Drought SC1103 PI576434 Nigeria SC1345 PI597980 Mali C=0.8 ; G=0.1 SC265 PI533766 Burki Faso G=1 SC283 PI533869 Tanzania K=0.7 ; G=0.3 Aluminum SC35 PI534133 Ethiopia D=0.8 ; K=0.1 Stay-‐Green SC971 PI656111 Puerto Rico K=0.5 ; G=0.3; C=0.2 Segaolane PI656023 Botswana K=1 Fig. 1 SchemaQc diagram of sorghum NAM development [14]
Founders PCA2 (9%)
The Nested AssociaQon Mapping design that consists in a joint analysis of several Recombinant Inbred Lines (RILs) families [1] improves the allelic diversity captured, resoluQon (low LD) and power of QTL detecQon. The historical populaQon structure of the species that is an obstacle to adapQve traits dissecQon in associaQon studies is actually reshuffled during RILs development. The aim of this study was to develop a genomic resource for the sorghum NAM and evaluate the power of the sorghum NAM to dissect the architecture of key traits such as flowering Qme and plant height.
Table. 1 InformaQon about the founders
SC283
Kafir Durra Guinea Caudatum
Macia P898012 SC1345 SC265 Ajabsido SC35
SC1103
SC971
Segaolane 0
PCA1 (10%) Fig. 2 PCA* represenQng the SAP panel and the founders
RTx430 0.1
Fig. 3 Dendrogram represenQng RILs dissimilariQes, different colors corresponding to families
Results
v The founders captured 74% of allelic variaQon compared to the SAP panel (Fig. 1). Progenies of each family were approximately equally related to each other (Fig. 3). 8.4% of markers showed segregaQon distorQons (P-‐ value < 0,001) (Fig. 4) which is superior to maize NAM observaQons [4]. v Plant height values and variances were smaller in the semi-‐arid environment (Fig. 5). v Dw1 and Dw3 were the main QTLs for PTHT as observed previously [5-‐8]. We confirmed that Dw1 (chr9) fracQonates into separate QTLs for FT and PTHT 9]. Dw2 (chr6) that is monomorphic in conversion lines [9-‐10] was associated with PTHT in the NAM as shown in previous associaQon studies [8]. It was also associated with FT. We observed a major QTL strongly associated with FT on chromosome 3 (Fig. 6). v Some other QTLs were specific to some families (Table. 2). v Polygenic variances were 65%, 74% and 55% for FT and PTHT conQnental-‐ humid and semi-‐arid respecQvely.
-log10 (P-value)
Flowering Time (continental humid)
Plant Height (continental humid) Dw3
Ma1
SbCN12/ HD3A
Fig. 6a
Plant Height (semi-arid)
Dw1 Dw1 Dw3
SbFL9.1
Dw2
Fig. 6b
Dw2
Fig. 6c
Fig. 6 ManhaLan plots of associaQons obtained for (a) FT and PTHT in a (b) conQnental-‐humid or (c) semi-‐arid environment
Discussion
Fig. 3 SegregaQon distorQon: heatmap represenQng for each marker the proporQon of lines carrying Tx430 allele in red or the alternate in blue
Table. 2 Major QTLs Marker (V2) Trait S3_55561782 FT S6_41868858 FT S6_42770899 PTHT S7_58688342 PTHT S8_53154668 PTHT sa S9_57008185 PTHT S9_56769620 PTHT S9_59327704 FT S10_38630941 FT S10_14351996 FT
Flowering Time (days to anthesis)
Fig. 4 Genetic map distance (y axis) versus physical map distance (x axis)
Plant Height (cm)
LOD Family 5.2 6 9 3,10 11.4 8 9 1 4.5 3 10.8 1,3,4,9,10 10.8 1,2,4,9,10 5.5 9 6 8 5.9 8,10
Families indexes: 1-Ajabsido, 2-Macia, 3- P898012, 4SC1103, 5-SC1345, 6-SC265, 7-SC283, 8-SC35, 9-SC971, 10-segaolane. PTHT sa stands for PTHT measured in the semi-arid environment. Marker names correspond to chromosome and physical position in bp on Sorghum genome sequence version 2.
v The lack of diversity/recombinaQon on chromosome 6 in converted lines limits adapQve potenQal for at least 7 major traits including 4 disease traits [11]. The NAM that was built with SCP and non-‐SCP lines decently circumvents this issue. It is a promising tool for deciphering the architecture of many traits for both forage and grain sorghum, with high resoluQon and power, thanks to high-‐throughput phenotyping and genotyping. v PTHT (dwarfism) and FT (photoperiod insensiQvity) have been the main targets of selecQon for the recent sorghum adaptaQon to temperate laQtudes and mechanized harvest [12-‐13]. Deciphering the architecture of flowering Qme and correlated traits will help guide more efficient marker-‐directed conversion of exoQc lines or adjustments of current elite lines to new environments.
Fig. 5a
Fig. 5b
Fig. 5 Phenotypic distribuQon for (a) FT and (b) PTHT in each family. Black dots stand for the phenotypes of the common parent Tx430 and red dots stand for the phenotypes of the alternate parents. Black verQcal lines stand for the global mean and red verQcal lines stand for the family mean, dashed and dot lines for humid-‐conQnental and semi-‐arid environments respecQvely.
References
[1] Buckler et al., 2009; [2] Glaubitz et al., 2014; [3] Browning and Browning 2007; [4] McMullen et al., 2009; [5] Lin et al., 1995; [6] Pereira and Li 1995; [7] Brown et al., 2008; [8] Morris et al., 2013; [9] Thurber et al., 2013; [10] Klein et al., 2008; [11] Mace et al., 2010; [12] Stephens et al., 1967; [13] Jordan et al., 2011; [14]. Yu et al., 2013 in Genomics of the Saccharinae; [15] Yang et al., 2011; [16] Broman et al., 2003.. 111
AbbreviaQons
NAM: Nested AssociaQon Mapping; SAP: Sorghum AssociaQon Panel; RIL: Recombinant Inbred Line; QTL: QuanQtaQve Trait Locus; GWAS: Genome Wide AssociaQon Studies;PCA: Principal Component Analysis; FT: Flowering Time; PTHT: Plant Height .
