Background
Interrelationship between growth habit and flowering played a key role in the domestication history of pulses; however, the actual genes responsible for these traits have not been identified in Indian bean. Determinate growth habit is desirable due to its early flowering, photo-insensitivity, synchronous pod maturity, ease in manual harvesting and short crop duration. The present study aimed to identify, characterize and validate the gene responsible for growth habit by using a candidate gene approach coupled with sequencing, multiple sequence alignment, protein structure prediction and binding pocket analysis.
Results
Terminal flowering locus was amplified from GPKH 120 (indeterminate) and GNIB-21 (determinate) using the primers designed from PvTFL1y locus of common bean. Gene prediction revealed that the length of the third and fourth exons differed between the two alleles. Allelic sequence comparison indicated a transition from guanine to adenine at the end of the third exon in GNIB 21. This splice site single-nucleotide polymorphism (SNP) was validated in germplasm lines by sequencing. Protein structure analysis indicated involvement of two binding pockets for interaction of terminal flowering locus (TFL) protein with other proteins.
Conclusion
The splice site SNP present at the end of the third exon of TFL locus is responsible for the transformation of shoot apical meristem into a reproductive fate in the determinate genotype GNIB 21. The splice site SNP leads to absence of 14 amino acids in mutant TFL protein of GNIB 21, rendering the protein non-functional. This deletion disturbed previously reported anion-binding pocket and secondary binding pocket due to displacement of small β-sheet away from an external loop. This finding may enable the modulation of growth habit in Indian bean and other pulse crops through genome editing.
Photoperiod responsive flowering and growth habit might
have played a key role in domestication of lablab bean
(Lablab purpureus) and currently shifting its cultivation
from intercropping to monoculture. Most of the landraces
of lablab bean exhibit photoperiod sensitivity in flowering
and indeterminate growth habit. A cross was made between
GNIB21 and GP189 which are phenotypic extremes for
photoperiod responsive flowering. The F1 hybrid exhibited
dominant traits like indeterminate growth habit and photosensitive
flowering endowed from male parent. Segregation
pattern of 3:1 in F2 generation indicated monogenic
recessive nature of photoperiod insensitive flowering. Bulk
segregant analysis in F2 population revealed association
of PvTFLy1, a locus governing determinate growth habit in
lablab bean, with photoperiod responsive flowering where
an amplicon of 300 bp was observed in photo sensitive
GP189 while it was absent in photo insensitive variety
GNIB21. Significant ÷2 test indicated coupling phase of
linkage between PvTFLY1 and photoperiod responsive
flowering. Linkage analysis placed PvTFLY1 at the distance
of 19.23 cM from the locus governing photoperiod
responsive flowering. The linkage between growth habit
and photoperiod responsive flowering in common bean,
soybean and Indian bean suggest that these traits may be
governed by mutation or deletion of E3 (or GmPhyA3) and
Dt1 homologs in Indian bean. Information available on
characterized genes for photoperiod responsive flowering
and determinate growth habit from common bean, soybean
and other related legumes may be utilized for isolation,
characterization, mapping and molecular dissection of
genes involved in regulation of photoperiod responsive
flowering in Indian bean.
Global agriculture is challenged with achieving sustainable food security while the climate changes and the threat of drought increases. Much of the research attention has focused on above-ground plant responses with an aim to improve drought resistance. The hidden half, that is, the root system belowground, is receiving increasing attention as the interface of the plant with the soil. Because roots are a sensing organ for nutrients and moisture, we speculate that crop root system traits can be managed using smart nutrient application in order to increase drought resistance. Roots are known to be influenced both by their underlying genetics and also by responses to the environment, termed root plasticity. Though very little is known about the combined effect of water and nutrients on root plasticity, we explore the possibilities of root system manipulation by nutrient application. We compare the effects of different water or nutrient levels on root plasticity and its genetic regulation, with a focus on how this may affect drought resistance. We propose four primary mechanisms through which smart nutrient management can optimize root traits for drought resistance: (1) overall plant vigor, (2) increased root allocation, (3) influence specific root traits, and (4) use smart placement and timing to encourage deep rooting. In the longer term, we envision that beneficial root traits, including plasticity, could be bred into efficient varieties and combined with advanced precision management of water and nutrients to achieve agricultural sustainability.
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