Special Issue "Impact of Genomics Technologies on Crop Breeding Strategies"

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A special issue of Agronomy (ISSN 2073-4395).

Deadline for manuscript submissions: closed (30 November 2011)

Special Issue Editors

Guest Editor
Prof. Dr. Peter Langridge

Australian Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, PMB 1, Glen Osmond, SA 5064, Australia
Website | E-Mail
Fax: +61 8 8303 7102
Interests: plant genomics; genetic engineering; cereal genetics
Guest Editor
Prof. Dr. J. Perry Gustafson

1-16 Agriculture, Division of Plant Sciences, College of Agriculture Food and Natural Resources University of Missouri, Columbia, MO 65211, USA
Website | E-Mail
Interests: plant breeding and genetics; plant genomics; cytology; evolution
Guest Editor
Dr. Rajeev K. Varshney

International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru-502 324, A.P., India
Website | E-Mail
Fax: +040 30713305
Interests: molecular markers; molecular breeding; gene discovery; applied genomics; legumes; abiotic stresses

Special Issue Information

Dear Colleagues,

Over the past few years we have seen a dramatic change in the resources and information available on crop genetics and genomics. In particular sophisticated molecular marker based strategies have been limited to the major crops and largely to large private sector breeding programs. The changes in DNA sequencing and development of SNP platforms as now changed this with many minor or orphan crops now able to access the same platforms. This special issue would provide a brief overview of breeding methodologies and strategies for a series of key crops.

The authors would be asked to explain current best practise in breeding for these crops with a specific examples from their breeding programs. They would also be asked to comment on the implication of new genetic and genomics technologies for
their crops, and how these technologies are likely to impact on their crop and what the key limitations to seeing delivery of new approaches are.

Prof. Dr. Peter Langridge
Prof. Dr. J. Perry Gustafson
Dr. Rajeev K. Varshney
Guest Editors

Keywords

  • breeding
  • genomics
  • selection
  • molecular markers
  • genome-wide selection
  • marker-assisted selection

Published Papers (7 papers)

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Research

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Open AccessArticle Impact of Molecular Genetic Research on Peanut Cultivar Development
Agronomy 2011, 1(1), 3-17; doi:10.3390/agronomy1010003
Received: 8 December 2011 / Revised: 20 December 2011 / Accepted: 20 December 2011 / Published: 20 December 2011
Cited by 7 | PDF Full-text (186 KB) | HTML Full-text | XML Full-text
Abstract
Peanut (Arachis hypogaea L.) has lagged other crops on use of molecular genetic technology for cultivar development in part due to lack of investment, but also because of low levels of molecular polymorphism among cultivated varieties. Recent advances in molecular genetic technology
[...] Read more.
Peanut (Arachis hypogaea L.) has lagged other crops on use of molecular genetic technology for cultivar development in part due to lack of investment, but also because of low levels of molecular polymorphism among cultivated varieties. Recent advances in molecular genetic technology have allowed researchers to more precisely measure genetic polymorphism and enabled the development of low density genetic maps for A. hypogaea and the identification of molecular marker or QTL’s for several economically significant traits. Genomic research has also been used to enhance the amount of genetic diversity available for use in conventional breeding through the development of transgenic peanut, and the creation of TILLING populations and synthetic allotetraploids. Marker assisted selection (MAS) is becoming more common in peanut cultivar development programs, and several cultivar releases are anticipated in the near future. There are also plans to sequence the peanut genome in the near future which should result in the development of additional molecular tools that will greatly advance peanut cultivar development. Full article
(This article belongs to the Special Issue Impact of Genomics Technologies on Crop Breeding Strategies)

Review

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Open AccessReview Impact of Genomic Technologies on Chickpea Breeding Strategies
Agronomy 2012, 2(3), 199-221; doi:10.3390/agronomy2030199
Received: 11 June 2012 / Revised: 10 August 2012 / Accepted: 13 August 2012 / Published: 23 August 2012
Cited by 18 | PDF Full-text (270 KB) | HTML Full-text | XML Full-text
Abstract
The major abiotic and biotic stresses that adversely affect yield of chickpea (Cicer arietinum L.) include drought, heat, fusarium wilt, ascochyta blight and pod borer. Excellent progress has been made in developing short-duration varieties with high resistance to fusarium wilt. The early
[...] Read more.
The major abiotic and biotic stresses that adversely affect yield of chickpea (Cicer arietinum L.) include drought, heat, fusarium wilt, ascochyta blight and pod borer. Excellent progress has been made in developing short-duration varieties with high resistance to fusarium wilt. The early maturity helps in escaping terminal drought and heat stresses and the adaptation of chickpea to short-season environments. Ascochyta blight continues to be a major challenge to chickpea productivity in areas where chickpea is exposed to cool and wet conditions. Limited variability for pod borer resistance has been a major bottleneck in the development of pod borer resistant cultivars. The use of genomics technologies in chickpea breeding programs has been limited, since available genomic resources were not adequate and limited polymorphism was observed in the cultivated chickpea for the available molecular markers. Remarkable progress has been made in the development of genetic and genomic resources in recent years and integration of genomic technologies in chickpea breeding has now started. Marker-assisted breeding is currently being used for improving drought tolerance and combining resistance to diseases. The integration of genomic technologies is expected to improve the precision and efficiency of chickpea breeding in the development of improved cultivars with enhanced resistance to abiotic and biotic stresses, better adaptation to existing and evolving agro-ecologies and traits preferred by farmers, industries and consumers. Full article
(This article belongs to the Special Issue Impact of Genomics Technologies on Crop Breeding Strategies)
Open AccessReview Impact of Molecular Technologies on Faba Bean (Vicia faba L.) Breeding Strategies
Agronomy 2012, 2(3), 132-166; doi:10.3390/agronomy2030132
Received: 10 May 2012 / Revised: 3 June 2012 / Accepted: 4 June 2012 / Published: 4 July 2012
Cited by 10 | PDF Full-text (303 KB) | HTML Full-text | XML Full-text
Abstract
Faba bean (Vicia faba L.) is a major food and feed legume because of the high nutritional value of its seeds. The main objectives of faba bean breeding are to improve yield, disease resistance, abiotic stress tolerance, seed quality and other agronomic
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Faba bean (Vicia faba L.) is a major food and feed legume because of the high nutritional value of its seeds. The main objectives of faba bean breeding are to improve yield, disease resistance, abiotic stress tolerance, seed quality and other agronomic traits. The partial cross-pollinated nature of faba bean introduces both challenges and opportunities for population development and breeding. Breeding methods that are applicable to self-pollinated crops or open-pollinated crops are not highly suitable for faba bean. However, traditional breeding methods such as recurrent mass selection have been established in faba bean and used successfully in breeding for resistance to diseases. Molecular breeding strategies that integrate the latest innovations in genetics and genomics with traditional breeding strategies have many potential applications for future faba bean cultivar development. Hence, considerable efforts have been undertaken in identifying molecular markers, enriching genetic and genomic resources using high-throughput sequencing technologies and improving genetic transformation techniques in faba bean. However, the impact of research on practical faba bean breeding and cultivar release to farmers has been limited due to disconnects between research and breeding objectives and the high costs of research and implementation. The situation with faba bean is similar to other small crops and highlights the need for coordinated, collaborative research programs that interact closely with commercially focused breeding programs to ensure that technologies are implemented effectively. Full article
(This article belongs to the Special Issue Impact of Genomics Technologies on Crop Breeding Strategies)
Open AccessReview Development of Genomic Resources in the Species of Trifolium L. and Its Application in Forage Legume Breeding
Agronomy 2012, 2(2), 116-131; doi:10.3390/agronomy2020116
Received: 9 February 2012 / Revised: 25 April 2012 / Accepted: 27 April 2012 / Published: 9 May 2012
Cited by 3 | PDF Full-text (260 KB) | HTML Full-text | XML Full-text
Abstract
Clovers (genus Trifolium) are a large and widespread genus of legumes. A number of clovers are of agricultural importance as forage crops in grassland agriculture, particularly temperate areas. White clover (Trifolium repens L.) is used in grazed pasture and red clover
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Clovers (genus Trifolium) are a large and widespread genus of legumes. A number of clovers are of agricultural importance as forage crops in grassland agriculture, particularly temperate areas. White clover (Trifolium repens L.) is used in grazed pasture and red clover (T. pratense L.) is widely cut and conserved as a winter feed. For the diploid red clover, genetic and genomic tools and resources have developed rapidly over the last five years including genetic and physical maps, BAC (bacterial artificial chromosome) end sequence and transcriptome sequence information. This has paved the way for the use of genome wide selection and high throughput phenotyping in germplasm development. For the allotetraploid white clover progress has been slower although marker assisted selection is in use and relatively robust genetic maps and QTL (quantitative trait locus) information now exist. For both species the sequencing of the model legume Medicago truncatula gene space is an important development to aid genomic, biological and evolutionary studies. The first genetic maps of another species, subterranean clover (Trifolium subterraneum L.) have also been published and its comparative genomics with red clover and M. truncatula conducted. Next generation sequencing brings the potential to revolutionize clover genomics, but international consortia and effective use of germplasm, novel population structures and phenomics will be required to carry out effective translation into breeding. Another avenue for clover genomic and genetic improvement is interspecific hybridization. This approach has considerable potential with regard to crop improvement but also opens windows of opportunity for studies of biological and evolutionary processes. Full article
(This article belongs to the Special Issue Impact of Genomics Technologies on Crop Breeding Strategies)
Open AccessReview Pea (Pisum sativum L.) in the Genomic Era
Agronomy 2012, 2(2), 74-115; doi:10.3390/agronomy2020074
Received: 13 December 2011 / Revised: 29 February 2012 / Accepted: 18 March 2012 / Published: 4 April 2012
Cited by 29 | PDF Full-text (2819 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Pea (Pisum sativum L.) was the original model organism used in Mendel’s discovery (1866) of the laws of inheritance, making it the foundation of modern plant genetics. However, subsequent progress in pea genomics has lagged behind many other plant species. Although the
[...] Read more.
Pea (Pisum sativum L.) was the original model organism used in Mendel’s discovery (1866) of the laws of inheritance, making it the foundation of modern plant genetics. However, subsequent progress in pea genomics has lagged behind many other plant species. Although the size and repetitive nature of the pea genome has so far restricted its sequencing, comprehensive genomic and post genomic resources already exist. These include BAC libraries, several types of molecular marker sets, both transcriptome and proteome datasets and mutant populations for reverse genetics. The availability of the full genome sequences of three legume species has offered significant opportunities for genome wide comparison revealing synteny and co-linearity to pea. A combination of a candidate gene and colinearity approach has successfully led to the identification of genes underlying agronomically important traits including virus resistances and plant architecture. Some of this knowledge has already been applied to marker assisted selection (MAS) programs, increasing precision and shortening the breeding cycle. Yet, complete translation of marker discovery to pea breeding is still to be achieved. Molecular analysis of pea collections has shown that although substantial variation is present within the cultivated genepool, wild material offers the possibility to incorporate novel traits that may have been inadvertently eliminated. Association mapping analysis of diverse pea germplasm promises to identify genetic variation related to desirable agronomic traits, which are historically difficult to breed for in a traditional manner. The availability of high throughput ‘omics’ methodologies offers great promise for the development of novel, highly accurate selective breeding tools for improved pea genotypes that are sustainable under current and future climates and farming systems. Full article
(This article belongs to the Special Issue Impact of Genomics Technologies on Crop Breeding Strategies)
Figures

Open AccessReview Genomic Databases for Crop Improvement
Agronomy 2012, 2(1), 62-73; doi:10.3390/agronomy2010062
Received: 11 January 2012 / Revised: 13 March 2012 / Accepted: 15 March 2012 / Published: 20 March 2012
Cited by 8 | PDF Full-text (180 KB) | HTML Full-text | XML Full-text
Abstract
Genomics is playing an increasing role in plant breeding and this is accelerating with the rapid advances in genome technology. Translating the vast abundance of data being produced by genome technologies requires the development of custom bioinformatics tools and advanced databases. These range
[...] Read more.
Genomics is playing an increasing role in plant breeding and this is accelerating with the rapid advances in genome technology. Translating the vast abundance of data being produced by genome technologies requires the development of custom bioinformatics tools and advanced databases. These range from large generic databases which hold specific data types for a broad range of species, to carefully integrated and curated databases which act as a resource for the improvement of specific crops. In this review, we outline some of the features of plant genome databases, identify specific resources for the improvement of individual crops and comment on the potential future direction of crop genome databases. Full article
(This article belongs to the Special Issue Impact of Genomics Technologies on Crop Breeding Strategies)
Open AccessReview Applied Genetics and Genomics in Alfalfa Breeding
Agronomy 2012, 2(1), 40-61; doi:10.3390/agronomy2010040
Received: 22 February 2012 / Revised: 2 March 2012 / Accepted: 6 March 2012 / Published: 15 March 2012
Cited by 15 | PDF Full-text (402 KB) | HTML Full-text | XML Full-text
Abstract
Alfalfa (Medicago sativa L.), a perennial and outcrossing species, is a widely planted forage legume for hay, pasture and silage throughout the world. Currently, alfalfa breeding relies on recurrent phenotypic selection, but alternatives incorporating molecular marker assisted breeding could enhance genetic gain
[...] Read more.
Alfalfa (Medicago sativa L.), a perennial and outcrossing species, is a widely planted forage legume for hay, pasture and silage throughout the world. Currently, alfalfa breeding relies on recurrent phenotypic selection, but alternatives incorporating molecular marker assisted breeding could enhance genetic gain per unit time and per unit cost, and accelerate alfalfa improvement. Many major quantitative trait loci (QTL) related to agronomic traits have been identified by family-based QTL mapping, but in relatively large genomic regions. Candidate genes elucidated from model species have helped to identify some potential causal loci in alfalfa mapping and breeding population for specific traits. Recently, high throughput sequencing technologies, coupled with advanced bioinformatics tools, have been used to identify large numbers of single nucleotide polymorphisms (SNP) in alfalfa, which are being developed into markers. These markers will facilitate fine mapping of quantitative traits and genome wide association mapping of agronomic traits and further advanced breeding strategies for alfalfa, such as marker-assisted selection and genomic selection. Based on ideas from the literature, we suggest several ways to improve selection in alfalfa including (1) diversity selection and paternity testing, (2) introgression of QTL and (3) genomic selection. Full article
(This article belongs to the Special Issue Impact of Genomics Technologies on Crop Breeding Strategies)

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