“Haplotype-led approaches for increasing precision in plant breeding”

   Climate change poses threats to resource-limited agriculture through altered pest-disease patterns and increasing abiotic stresses. The advent of rapid and cost-effective DNA sequencing has propelled large-scale germplasm sequencing initiatives and Genomics-assisted breeding (GAB). This has opened up promising avenues for harnessing haplotypes in breeding programs. Among various DNA markers, SNPs have gained prominence due to their abundance within plant genomes. However, their PIC value and biallelic nature have constrained the resolution of SNP-marker associations in comparison to SSR markers. To overcome this limitation, the construction of SNP-based haplotypes using LD has been proposed2.

Haplotypes are representing sets of SNPs on the same chromosome which are organized into blocks with minimal historical recombination, ensuring that polymorphic SNPs within a haplotype are inherited together. The HapMap, consisting of haplotype blocks and tagSNPs, facilitates the identification of these haplotypes. This approach equips crop breeders with strategies for haplotype exploration and its application in dissecting complex traits within the context of GAB. This includes haplotype-based GWAS, haplotype-centric breeding, and haplotype-assisted genomic selection. Effective deployment of superior haplotypes holds the potential to expedite breeding progress1.

In a study on pigeonpea, whole genome re-sequencing of 292 genotypes revealed superior haplotypes for 10 drought-responsive genes. 83, 132 and 60 haplotypes were identified across breeding lines, landraces, and wild species respectively. Association analysis on 137 accessions unveiled 23 strong marker-trait associations across five genes, influencing seven drought-responsive traits. Notably, promising four haplotypes C. cajan_23080-H2, C. cajan_30211-H6, C. cajan_26230-H11, and C. cajan_26230-H5 related to plant weight, fresh weight, turgid weight, and relative water content were exhibiting superiority under drought stress4.

In a study 383 wheat Genomic selection panel is phenotyped and genotyped for predicting GEBVs. Haplotype blocks of 5, 10, 15, and 20 adjacent markers were constructed for all chromosomes. In all cases, haplotype predictions outperformed single SNPs. Haplotypes of 15 adjacent markers showed the best improvement in accuracy for all traits. These results emphasize the effectiveness of using haplotypes in genomic selection to increase genetic gain3.

In conclusion, long-read sequencing accelerates valuable haplotype identification. Haplotype-based GWAS approaches with their precise identification of causal polymorphisms offers a robust alternative to SNP based GWAS. The superior efficiency of haplotypes in genomic prediction underscores their growing relevance in crop enhancement initiatives. Collectively, the integration of haplotype-based research holds great promise in routine cultivar development and bolstering future food security endeavors.

References: 

1. BHAT, J.A., YU, D., BOHRA, A., GANIE, S.A. AND VARSHNEY, R.K., 2021, Features and applications of haplotypes in crop breeding. Commun. Biol., 4(1): 1266. 

2. QIAN, L., HICKEY, L.T., STAHL, A., WERNER, C.R., HAYES, B., SNOWDON, R.J. AND VOSS-FELS, K.P., 2017, Exploring and harnessing haplotype diversity to improve yield stability in crops. Front. Plant Sci., 8: 1534. 

3. SALLAM, A.H., CONLEY, E., PRAKAPENKA, D., DA, Y. AND ANDERSON, J.A., 2020, Improving prediction accuracy using multi-allelic haplotype prediction and training population optimization in wheat. G3-GENES GENOM. GENET., 10(7): 2265-2273.

 4. SINHA, P., SINGH, V.K., SAXENA, R.K., KHAN, A.W., ABBAI, R., CHITIKINENI, A., DESAI, A., MOLLA, J., UPADHYAYA, H.D., KUMAR, A. AND VARSHNEY, R.K., 2020, Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea (Cajanus cajan L.). Plant Biotechnol. J., 18(12): 2482-2490.