Efficiency of honeycomb selection design and validation of molecular markers in early generation selection in rice

Breeding for salt tolerance is complex and tedious due to its genetics and environmental interaction. Honeycomb Selection Design (HSD), a paradigm for conventional breeding, provides an opportunity to breed density-independent cultivars under nil competition. The present study was attempted to study the effectiveness of HSD in selecting salt-tolerant genotypes in F2 and F3 populations of ADT (R) 45 × Nona Bokra rice cross raised in unreplicated honeycomb design (UN-1) in F2 generation and replicated honeycomb design (R-37) in F3 generation respectively at wider spacing of 100 cm x 90 cm. The F2 plants were selected based on plant index and F3 plants were selected based on plant and stability index. Plant index-based selection in F2 population identified 35 best performing genotypes accounting for 4.13 % selection intensity and they were forwarded to raise F3 population. In F3 population, 28 plants were selected based on plant index and stability index accounting for 3.63 % selection intensity. Such low selection intensity in HSD leads to rapid fixation of additive alleles that are indispensable for advancing through selection. In F2, 35 selected plants showed an increase of 213.86 % over the total mean of F2. Yield of F3 progenies significantly improved over the respective selected F2 plants showing positive genetic gain. In addition, the best performing 28 plants selected in F3 population were from 15 and 12 progeny lines in normal and saline condition among 35 individual entries selected in F2 population. Further, best 100 F2 and F3 plants were subjected to genotyping using nine markers linked to salt tolerance. The correlation between salt tolerance markers and observed morphological traits was weak in F2 which may be due to a lack of coverage of all the regions of salt tolerance quantitative trait loci (QTLs) and may also be due to unidentified regions of the chromosome conferring tolerance to salinity stress. Hence, selection for yield in the early generations (F₂ and F₃) of ADT (R) 45 × Nona Bokra rice cross using the HSD improves the efficiency of breeding procedure by reducing the number of genotypes to be tested in subsequent, expensive yield trials, thereby increasing genetic gain per unit cost.