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Genomics-assisted breeding for pigeonpea improvement

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Key message

The review outlines advances in pigeonpea genomics, breeding and seed delivery systems to achieve yield gains at farmers’ field.

Abstract

Pigeonpea is a nutritious and stress-tolerant grain legume crop of tropical and subtropical regions. Decades of breeding efforts in pigeonpea have resulted in development of a number of high-yielding cultivars. Of late, the development of CMS-based hybrid technology has allowed the exploitation of heterosis for yield enhancement in this crop. Despite these positive developments, the actual on-farm yield of pigeonpea is still well below its potential productivity. Growing needs for high and sustainable pigeonpea yields motivate scientists to improve the breeding efficiency to deliver a steady stream of cultivars that will provide yield benefits under both ideal and stressed environments. To achieve this objective in the shortest possible time, it is imperative that various crop breeding activities are integrated with appropriate new genomics technologies. In this context, the last decade has seen a remarkable rise in the generation of important genomic resources such as genome-wide markers, high-throughput genotyping assays, saturated genome maps, marker/gene–trait associations, whole-genome sequence and germplasm resequencing data. In some cases, marker/gene–trait associations are being employed in pigeonpea breeding programs to improve the valuable yield and market-preferred traits. Embracing new breeding tools like genomic selection and speed breeding is likely to improve genetic gains. Breeding high-yielding pigeonpea cultivars with key adaptation traits also calls for a renewed focus on systematic selection and utilization of targeted genetic resources. Of equal importance is to overcome the difficulties being faced by seed industry to take the new cultivars to the doorstep of farmers.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

BES:

BAC-end sequence

CAPS:

Cleaved amplified polymorphic sequence

CcGEA:

Cajanus cajan gene expression atlas

CMS:

Cytoplasmic nuclear male sterility

CNV:

Copy number variation

DArT:

Diversity arrays technology

EST:

Expressed sequenced tag

FW:

Fusarium wilt

GBS:

Genotyping-by-sequencing 

GEBV:

Genomic estimated breeding value

GMS:

Genic male sterility

GoT:

Grow-out test

GWAS:

Genome-wide association study

LTR:

Long terminal repeat

InDel:

Insertion/deletion

MABC:

Marker-assisted backcrossing

MAGIC:

Multiparent advanced generation intercross

MAS:

Marker-assisted selection

MTA:

Marker–trait association

NAM:

Nested association mapping

NGS:

Next-generation sequencing

ns:

Nonsynonymous

ORFs:

Open reading frames

PAV:

Presence/absence variation

QTL:

Quantitative trait loci

RADSeq:

Restriction site-associated DNA sequencing

RAPD:

Random amplified polymorphic DNA

RE:

Repeat element

RF:

Restoration of fertility

RFLP:

Restriction fragment length polymorphism

RGT:

Rapid generation turnover

RIL:

Recombinant inbred line

SB:

Speed breeding

SBB:

Sequence-based breeding

Seq-BSA:

Sequencing-based bulked segregant analysis

SMD:

Sterility mosaic disease

SNP:

Single-nucleotide polymorphism

SPC:

Seed protein content

SRR:

Seed replacement rate

SSR:

Simple sequence repeat

SV:

Structural variation

TAC:

Transcript assembly contig

TGMS:

Temperature-sensitive genic male sterility

VRR:

Variety replacement rate

WGRS:

Whole-genome resequencing

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Acknowledgements

AB acknowledges support from Centre for Agricultural Bioinformatics (CABin: AGENIASRICOP201501000047) scheme of Indian Council of Agricultural Research (ICAR), New Delhi. Authors are also thankful for the Department of Agriculture Cooperation & Farmers Welfare, Ministry of Agriculture & Farmers Welfare, Government of India, Ministry of Agriculture, Government of Karnataka for funding various pigeonpea research projects. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC). ICRISAT is a member of CGIAR Consortium.

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  1. K. B. Saxena

    Present address: , 17, NMC Housing, Al Ain, Abu Dhabi, United Arab Emirates

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  1. ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India

    Abhishek Bohra

  2. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India

    Rajeev K. Varshney & Rachit K. Saxena

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  1. Abhishek Bohra
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AB and RKS conceived and outlined the review. AB, RKS and RKV wrote the manuscript. KBS contributed special sections. All authors read and approved the final manuscript.

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Bohra, A., Saxena, K.B., Varshney, R.K. et al. Genomics-assisted breeding for pigeonpea improvement. Theor Appl Genet 133, 1721–1737 (2020). https://doi.org/10.1007/s00122-020-03563-7

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