GENOME WIDE ASSOCIATION STUDIES FOR GRAIN IRON AND ZINC CONTENTS IN CHICKPEA (Cicer arietinum L.)
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Date
2024-05-01
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Acharya N G Ranga Agricultural University
Abstract
Chickpea is a cheap source of protein and micronutrients to the poor people
living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa and
contribute towards reducing malnutrition resulting from protein and micronutrient
deficiency. The current study evaluated chickpea reference set of 280 accessions
(landraces, breeding lines, and advanced cultivars) to study the variability, diversity
and to delineate the genetic nature of grain nutrient (protein, Fe, Zn content) and
agronomic traits in normal (NS) and heat stress (HS) conditions using genome-wide
association studies. The analysis of variance (ANOVA) revealed highly significant
difference among the accessions for grain nutrients and agronomic traits under normal
and heat stress seasons. Genetic diversity studies revealed a wide range of variability
for grain protein (15.7–25.3%), Fe (44.8–74.9 mg kg-1
) and Zn (38.4–65.7 mg kg-1
)
contents along with agronomic traits. The accessions, ICC 9848 (NS-Protein: 26.21%,
Fe: 76.74 mg kg-1
, Zn: 55.74 mg kg-1
; HS-Protein: 25.25%, Fe: 65.52 mg kg-1
, Zn:
59.71 mg kg-1
), ICC 9895 (NS-Protein: 25.49%, Fe: 75.65 mg kg-1
, Zn: 52.48 mg kg 1
; HS-Protein: 24.19%, Fe: 70.90 mg kg-1
, Zn: 59.92 mg kg-1
), ICC 9862 (NS-Protein:
25.69%, Fe: 72.78 mg kg-1
, Zn: 52.53 mg kg-1
; HS-Protein: 24.85%, Fe: 67.74 mg kg 1
, Zn: 63.27 mg kg-1
) and ICC 9872 (NS-Protein: 25.70%, Fe: 69.85 mg kg-1
, Zn:
52.46 mg kg-1
; HS-Protein: 25.13%, Fe: 73.84 mg kg-1
, Zn: 63.27 mg kg-1
) were
found promising for grain protein, Fe and Zn content across the environments. The
kabuli accessions showed high average grain protein and Fe content when compared
with the desi types. The PCV and GCV of nutrient traits was low to moderate across
the environments. High heritability was noted for all the traits under individual
seasons of normal and heat stress whereas pooled seasons noted moderate heritability
for grain Fe and Zn contents. High heritability with high GAM was recorded for days
to first flower, days to 50% flowering, plant height, number of filled pods per plant,
number of unfilled pods per plant, number of pods per plant, number of seeds per
plant, 100 seed weight, harvest index and seed yield across the environments. The
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association among the nutrient traits across the environments was positive and was
negative with seed yield. The principal component analysis revealed first four PCs
under normal season1 (NSI) and three PCs under normal season2 (NSII), Pooled and
heat stress (HS) contributed maximum per cent of total variation for nutrient and
agronomic traits. Cluster analysis grouped the accessions into two clusters across the
environments. GT biplot identified the accessions, ICC 9848, ICC 9872, ICC 9895
and ICC 9862 with high grain protein and Fe content; ICC 1161, ICC 8522 and ICC
2242 with high Zn content; and ICC 6874 and ICC 1392 with high values for seed
yield over the seasons. The genotyping of chickpea reference set using mid-density 5k
SNP array panel resulted in 4603 highly informative SNPs distributed across the
chickpea genome. Population structure analysis revealed three subpopulations (K=3)
in the reference set. PCA using SNP markers data revealed three distinct clusters
where PC1 explained 38.2% and PC2 revealed 9.31% of total variance. The
unweighted neighbor-joining (NJ) tree method grouped the accessions into three
clusters. Linkage disequilibrium (LD) was extensive across the chickpea genome and
LD decay was relatively low at a physical distance of 4032Kb across the genome.
Genome-wide association analysis revealed a total of 20 and 73 marker-trait
associations (MTAs) for grain nutrient and agronomic traits over normal seasons
while a total of 11 and 45 MTAs were significantly associated with grain Fe and
agronomic traits under HS using FarmCPU and BLINK models. The marker,
S4_4477846 on chr4, was found to be co-associated with grain protein over seasons.
The markers, S1_11613376 and S1_2772537 on chr1, co-associated with grain Fe
content under NSII and pooled seasons and the marker, S7_9379786 on chr7, was co associated with grain Fe content under NSI, pooled and HS. SNP annotation of
associated markers was found to be related to gene functions of metal ion binding,
transporters, protein kinases, transcription factors, and many more functions involved
in plant metabolism along with Fe and protein homeostasis. The identified significant
MTAs require further validation and characterization to elucidate the exact role of
these genes in chickpea. Further, it was noted, 92.9%, 74.3% and 10.4% of the
accessions showed reduction of ~25% of grain protein, 22% of Fe and 16% of Zn
under heat stress. The accessions, ICC 9848, ICC 9895, ICC 9862 and ICC 9872 were
least affected by heat for protein, ICC 9895 and ICC 9643 for grain Fe content can be
exploited in breeding programmes to develop nutrient-rich climate resilient chickpea
cultivars. The present study highlighted the use of chickpea reference set for
exploitation in marker-assisted selection to develop nutrient dense climate resilient
chickpea varieties