Genetic Diversity Analysis and QTL Mapping of Selected Traits in Sorghum (Sorghum Bicolor (L.) Moench
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Date
2016-05-05
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Addis Ababa University
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is one of the most important multipurpose crops grown
globally. It can be used as food, feed, fiber and biofuel feedstock. In Ethiopia, sorghum is among
the most important cereal crops accounting for 18 % of annual production and 16 % of land
cover allocated to the entire grain crops including cereals, pulses and oilseeds. Despite this
importance and huge potential as bioenergy feedstock, detailed study on characterization,
identification and mapping of novel genes that code for sugar content related and drought
tolerance traits using Ethiopian sorghum was lacking. Therefore, this study is aimed at
germplasm collection, characterization, and identification and mapping of novel QTLs using both
grain and sweet type of sorghum germplasm of Ethiopia. Both morphological and molecular
evaluation of Ethiopian sweet sorghum germplasm was undertaken. Genotyping of 175 Ethiopian
sweet sorghum genotypes alongside 27 improved accessions from eastern and southern Africa
was undertaken. Two independent experiments were also carried out to identify and map QTLs
associated to Brix and stay-green related traits using F2:3 segregating mapping populations
derived from a cross between grain sorghum with stay-green feature (Sorcoll 163/07) and sweet
sorghum (Gambella). A genetic map was constructed using 192 F2 populations genotyped with 76
SSR markers. Research was carried out to screen and compile the most informative SSR markers
across some accessions. A total of 304 markers were used to identify the most polymorphic SSR
markers across eleven farmers preferred sorghum genotypes. Combined analysis of variance for
Brix and other morphological characters to evaluate 181 sweet sorghum accessions collected
from the major producing regions of Ethiopia showed that there is a significant effect of the
environment on all tested traits. Mean separation analysis revealed that collections from northern
Ethiopia were found to be superior in terms of Brix degree. Collections from the rest of collection
regions showed relatively low Brix mean value but characterized by higher biomass. Broad sense
heritability estimate showed most characters are highly heritable except grain yield. Pearson
correlation coefficients (r) of the seven traits presented Brix degree was negatively correlated to
most of the traits. Cluster analysis based on the Brix and other morphological characters grouped
the accessions into five clusters. The constructed dendrogram based on mean of collection zones
for the tested traits also clearly put adjacent regions or zones together. All the tested markers
detected 159 alleles and a high degree of polymorphism information content (PIC) averaging
0.69. A comparison between Ethiopian and improved accessions revealed higher allele numbers
(124) in Ethiopian than improved accessions (92 alleles). More than half (65 out of 124) of the
alleles observed in the Ethiopian accessions were rare (<5%) while 64 were private (only present
within Ethiopian accessions) while in the improved accessions, 41% and 38% of the alleles
detected were rare and private respectively. Both weighted Neighbor Joining-based clustering
and hierarchical clustering grouped the 202 accessions into three major clusters based on
geographical origin. Ethiopian accessions from the north (Wello and south Tigray) not only
clustered separately from accessions from the west central and eastern Ethiopia, but were also
distinct from most of the improved genotypes. A total of seven QTLs distributed across five
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linkage groups that controls Brix content were detected using Inclusive Composite Interval
Mapping (ICIM). Each QTL contributed 17.2 to 44.3% of the total phenotypic variation. Using
the same genotypic data ICIM detected two stay-green QTLs using F2:3 populations evaluated
under regulated irrigation supply. Four QTLs distributed on linkage groups SBI-01, SBI-06, SBI-
08 and SBI-09 were detected under rain fed drought prone environment. Three QTLs that
controls chlorophyll content also detected on SBI-03, SBI-06 and SBI-07. Out of the total SSRs
used across eleven farmers preferred sorghum genotypes, nearly half of the markers 139 (45.7%)
detected 543 alleles and a high degree of polymorphism information content (PIC) averaging
0.53.The overall observed heterozygosity (Ho) over loci varied from 0.00 to 1.00 with an average
of 0.16. Nearly 60 % (83 markers) have showed zero value of the Ho. The gene diversity index
(expected heterozygosity, He) ranged from 0.17 to 0.91 with a mean of 0.58. Weighted neighborjoining
cluster analysis grouped the genotypes into three distinct groups. All genotypes with staygreen
future (B 35, Sorcoll 163/07, E 36-1 and Sorcoll 141/07) were clustered together.
Genotypes such as Gambella, Macia, 76T#23, Meko and Melkam were distinct from the rest of
the genotypes and grouped together. The third group consists of Teshale and Sorcoll 146/07. The
results from both morphological and molecular based evaluation reveal an unexploited highly
diverse sweet sorghum genetic resource from Ethiopia that can be more efficiently included in the
regional breeding programs in order to efficiently optimize productivity. Co-localization of staygreen
QTL with QTLs for chlorophyll content in two environments has the implication that the
two traits were governed by genes found on same linkage group and useful QTLs to be used in
breeding program in the future. The current study forms an essential foundation for future grain
and sweet sorghum breeding programs of the country as well as for ongoing programs at
International Crop Research Institutes for Semi-Arid Tropics.
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Keywords
Genetic Diversity Analysis, QTL Mapping of Selected, Traits in Sorghum