Sorghum is the fifth most important C4 cereal crop grown globally in arid and semi-arid climatic conditions. Drought is the major cause for loss of productivity worldwide. Delayed senescence of plants leads to adaptation to drought stress conditions by staying-green and giving high yields. In order to identify and dissect the stay-green genomic regions we have developed a high resolution fine mapping population from introgression line cross RSG04008-6 (stay-green) × J2614-11 (shoot fly resistant). Nearly 1894 F2 genotypes were screened with 8 SSR in order to identify double recombinants for both the parents in the sorghum chromosome-10 long arm (SBI-10L).

1. Fine mapping of stay-green QTLs on sorghum chromosome SBI-10L
‒ An approach from Genome to Phenome
Usha Kiranmayee K N S1, 2*, Hash C T 3, Kavi Kishor P B2, Ramu P4, Sivasubramani S1, Santosh P Deshpande1
1 International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
2 Department of Genetics, Osmania University, Hyderabad, India
3 International Crop Research Institute for the Semi-Arid Tropics, Niamey, Niger
4 Cornell university, Ithaca, New York, United States
*E-mail: knskira@gmail.com
Abstract Sorghum is the fifth most important C4 cereal crop grown globally in arid and semi-arid climatic conditions. Drought is the major cause for loss of productivity worldwide.
Delayed senescence of plants leads to adaptation to drought stress conditions by staying-green and giving high yields. In order to identify and dissect the stay-green genomic
regions we have developed a high resolution fine mapping population from introgression line cross RSG04008-6 (stay-green) × J2614-11 (shoot fly resistant). Nearly 1894 F2
genotypes were screened with 8 SSR in order to identify double recombinants for both the parents in the sorghum chromosome-10 long arm (SBI-10L). The selected F2:4
recombinants were GBSed to increase the marker density between flanking markers Xgap001-Xtxp141 for stay-green QTLs on SBI-10L and a high resolution linkage map was
developed using GBS SNPs. Out of 182 only 152 recombinants were replicated thrice in field for stay-green screening for two seasons (Summer 2013 and 2014). Fine mapping
of the per cent Green Leaf Area (%GLA) traits identified 33 QTLs and 19 QTLs were clustered into 7 groups where 8 genes were identified. These were AP2/ERF transcription
factor family (Sb10g025053), Ankyrin-repeat protein (Sb10g025310), WD40 repeat protein (Sb10g025320), NBS-LRR Protein (Sb10g025283), Calcium dependant protein kinase
(Sb10g030150), LEA2 protein (Sb10g029570), a putative uncharacterized protein (Sb10g024920) and senescence associated protein (Sb10g030520). With this study SBI-10L
stay-green genomic regions were delimited from 15Mb to 8 genes co-localized with GWAS MTAs. Further cloning and expression level studies of the identified candidate genes
will improve the development of drought tolerant genotypes.
cQTL Nearest marker
position
cM
marker
Intervals
No. of
QTLs
Integrated QTLs
Gene
ID/MTAs
Combined
R2
Candidate genes SNP effect
cQstg10.1 S10_54269620 36.41 36.41 3
Q10GLA14a_14,Q10GLA2
8a_14.Q1049a_across
Sb10g025053
12.4
AP2/ERF transcryptional
factor
Intergenic
cQstg10.2 S10_54081973 41.41 39.8 – 42.8 4
Q10GLA7a_13,Q10GLA14
a_13,Q10GL21b_13,Q10G
LA28b_14
Sb10g024920 31.3
weakly similar to Putative
uncharacterized protein
non
synonymous
cQstg10.3 S10_54535306 45.01 42.8 – 47.4 2
Q10GLA7a_across,Q10GL
A14a_across
Sb10g025283 16.95
NBS-LRR disease resistance
protein
Synonimous
&non
synonimous
(Exonic
region)
cQstg10.4 S10_54585199 44.41 54.58- 54.59 2
Q10GLA14b_14,Q10GLA4
9b_across
Sb10g025310,
320
10.57
Ankyrin repeat protein and
WD40 repeat family protein
(trasducin protein)
Intron
cQstg10.5 S10_59342820 115.31
114.5 – 115.6
3
Q10GLA21a_13,Q10GLA2
1a_14,Q10GLA21a_acros
s
Sb10g029570 28
similar to Putative
uncharacterized protein
P0655A07.24/LEA
Synonimous
&non
synonimous
(Exonic
region)
cQstg10.6 S10_59775456 120.6 121.4 ‒ 122.5 2
Q10GL35a_13,Q10GLA42
a_13
Sb10g030040 6.58
Ca/calmodulin dependant
protein kinase
Intron
cQstg10.7 S10_60194379 125.01 124.7 – 125.5 3
Q10GL21c_13,Q10GLA28
a_13,Q10GLA28a_across
Sb10g030520 5.5
similar to Senescence-
associated protein
3'UTR+
Exon
Sorghum gene ID Description Functional role Reference
Sb10g025053 AP2/ERF transcryption factor
Over expression of AP2/ERF family genes have been shown to
improve stress tolerance under water defect conditions
Mawlong et al.,
2015
Sb10g025310 Ankyrin repeat protein involved during flower senescence Xu et al., 2007
Sb10g025320
Transducin family protein/
WD40 repeat protein
involved in senescence mechanism Guo and Gan, 2012
Sb10g025283 NBS-LRR protein gene
Defense response protein leads to increased levels of SA, ABA
and cytokinin
Sarazin et al., 2015
Sb10g029570 LEA2 protein
reported to play a role in late embryogenesis and drought stress
mechanisms
Gao and Lan, 2016
Sb10g030040 Calcium/calmodulin dependant protein kinase
plays a functional role in the identification of drought tolerant
locus
Franz et al., 2011
Sb10g030520 Senescence associated protein kinase Reported to be involved in senescence mechanisms Liang et al.,2014
Sb10g030770 No apical meristem (NAM) protein
Increased expression of NAC transcriptional factors leads to
drought stress tolerance
Zaho et al ., 2015
Sb10g030776 Starch branching enzyme I precursor Glycogen biosynthesis in seed Peleg et al., 2011
Sb10g031030 similar to Putative AGO1 homologous protein Controls miRNA168 mediated drought tolerance Wang et al., 2014
Sb10g026180,
Sb10g029530
similar to Pentatricopeptide (PPR) repeat-
containing protein-like
involved in chlorophyll degradation mechanism by stabilizing
RNA in chloroplasts
Manna et al., 2015
Sb10g027640 WRKY transcription factor over expression lead to drought tolerance in rice Cai et al., 2015
Sb10g029810 MADS box transcription factors
alterations may lead to stay-green which is involved in many
developmental processes
Shore and
Sharrocks, 1995
Sb10g030620 Exocyst subunit
involved in auto phagosome/autolysis associated in
programmed cell death
Lim et al., 2007
Sb10g026200
Squamosa binding protein family
transcriptional factors
reported to be involved in leaf, flower, fruit and vegetative
phase developmental stages
Preston and
Hileman, 2013
Sb10g028300 Zinc finger reported to be involved in senescence Griffith et al., 2014
Sb10g022580
CYTOKININ-RESPONSIVE
GATA FACTOR 1
involved in chloroplast metabolism Hudson et al., 2013
STAY-GREEN PUTATIVE CANDIDATE GENES
STAY-GREEN QTL CLUSTERS ON SBI-10L FINE MAPPING OF STAY-GREEN TRAIT ON SBI-10L
WORK FLOW SNP eff on SBI-10L SSR MAP INTEGRATED WITH 260 GBS-SNPs
Conclusions
• GBS-SNP analysis resulted in identification of genomic regions having candidate genes associated for stay-green trait on chromosome
SBI-10L.
• In addition, this identified a huge number of SNPs that can be useful for genomics-assisted sorghum breeding.
• Further cloning and expression studies of the significantly associated candidate genes may reveal the appropriate role in the biological
processes associated with the stay-green (component of both terminal drought tolerance and ruminant livestock feeding value of stover)
and can be involved in development of drought tolerant varieties.
Acknowledgements
• This work is part of PhD work from Department of Genetics, Osmania university
Hyderabad
• Financial support from ICRISAT ‘s Dryland Cereals research program is greatly
acknowledged.
• This work has been undertaken as part of the CGIAR Research Program - Dryland Cereals/
Genetic Gains.
Horseshoe effect of SNPs Distance matrix of SNPs
Usha Kiranmayee K N S1, 2*
, Hash C T 3
, Kavi Kishor P B2
, Ramu P4
, Sivasubramani S1
, Santosh P Deshpande1
1
International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
2
Department of Genetics, Osmania University, Hyderabad, India
3
International Crop Research Institute for the Semi-Arid Tropics, Niamey, Niger
4
Cornell university, Ithaca, New York, United States
* Email: knskira@gmail.com
Fine Mapping of stay-green QTLs on sorghum chromosome
SBI-10L – An approach from Genome to Phenome
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Feb
2017