J. C. Dawson

Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing

Genomic selection (GS) uses genomewide molecular markers to predict breeding values and make selections of individuals or breeding lines prior to phenotyping. Here we show that genotyping‐by‐sequencing (GBS) can be used for de novo genotyping of breeding panels and to develop accurate GS models, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS we discovered 41,371 single nucleotide polymorphisms (SNPs) in a set of 254 advanced breeding lines from CIMMYTs semiarid wheat breeding program. Four different methods were evaluated for imputing missing marker scores in this set of unmapped markers, including random forest regression and a newly developed multivariate‐normal expectation‐maximization algorithm, which gave more accurate imputation than heterozygous or mean imputation at the marker level, although no significant differences were observed in the accuracy of genomic‐estimated breeding values (GEBVs) among imputation methods. Genomic‐estimated breeding value prediction accuracies with GBS were 0.28 to 0.45 for grain yield, an improvement of 0.1 to 0.2 over an established marker platform for wheat. Genotyping‐by‐sequencing combines marker discovery and genotyping of large populations, making it an excellent marker platform for breeding applications even in the absence of a reference genome sequence or previous polymorphism discovery. In addition, the flexibility and low cost of GBS make this an ideal approach for genomics‐assisted breeding.

Decentralized selection and participatory approaches in plant breeding for low-input systems

Heterogeneous environments make it difficult to apply consistent selection pressure because often it is difficult to identify a single or a few superior genotypes across all sets of conditions. However, when the target system is characterized by heterogeneity of environmental stress, varieties developed in high-yielding conditions may fail to satisfy farmers’ needs. Although this type of system is often found in marginal environments of developing countries, heterogeneous environmental conditions are also a feature of organic and low-external-input systems in developed countries. To meet the needs of these systems, breeding programs must decentralize selection, and although decentralized selection can be done in formal breeding programs, it is more efficient to involve farmers in the selection and testing of early generation materials. Breeding within these target systems is challenging, both genetically and logistically, but can identify varieties that are adapted to farming systems in marginal environments or that use very few external inputs. A great deal has been published in recent years on the need for local adaptation and participatory plant breeding; this article reviews and synthesizes that literature.

Seed exchanges, a key to analyze crop diversity dynamics in farmer-led on-farm conservation

Sustainable management of genetic resources is a crucial issue in the global context of food security. On-farm conservation is now widely acknowledged as a relevant strategy to reach this goal because it maintains evolutionary forces within and between the different components of the agricultural system. Seed exchanges between farmers play a key role in this process but are complicated to study over different agricultural contexts. This review begins by illustrating how interdisciplinary approaches combining ethnobotany and genetics helps provide a detailed analysis of the role of social and genetic dynamic interactions related to seed exchanges in traditional farming systems with farmer-led on-farm conservation. Secondly, the evolution of crop genetic diversity management is described in the context of industrialized farming systems. We follow the evolution of crop biodiversity perception by involved actors using a socio-historical perspective. After the agricultural shift from a traditional to a productivist model, recent social developments such as citizen science and participatory research movements are emerging and are strongly concerned by the question of biodiversity. These emerging trends which recognize and value seed exchanges between farmers show similarities to farmer-to-farmer seed exchanges in traditional farming systems. To what extent are these systems comparable? To fully benefit from studies in both traditional and industrialized contexts, it will be critical to develop an interdisciplinary framework to rigorously compare seed exchange systems and more generally farmer-led on-farm conservation strategies in diverse agricultural systems.

On-farm dynamic management of genetic diversity: the impact of seed diffusions and seed saving practices on a population-variety of bread wheat

Since the domestication of crop species, humans have derived specific varieties for particular uses and shaped the genetic diversity of these varieties. Here, using an interdisciplinary approach combining ethnobotany and population genetics, we document the within‐variety genetic structure of a population‐variety of bread wheat (Triticum aestivum L.) in relation to farmers’ practices to decipher their contribution to crop species evolution. Using 19 microsatellites markers, we conducted two complementary graph theory‐based methods to analyze population structure and gene flow among 19 sub‐populations of a single population‐variety [Rouge de Bordeaux (RDB)]. The ethnobotany approach allowed us to determine the RDB history including diffusion and reproduction events. We found that the complex genetic structure among the RDB sub‐populations is highly consistent with the structure of the seed diffusion and reproduction network drawn based on the ethnobotanical study. This structure highlighted the key role of the farmer‐led seed diffusion through founder effects, selection and genetic drift because of human practices. An important result is that the genetic diversity conserved on farm is complementary to that found in the genebank indicating that both systems are required for a more efficient crop diversity conservation.

Social and political influences on agricultural systems

Agricultural systems are situated within social and political environments that have tremendous influence on how they operate. If agricultural systems are to be sustainable, it is critical to understand how they are influenced by social and political factors. An expert panel approach was used to identify and rank the importance of social and political factors on agricultural systems in the US and to provide some insights into their impacts, interactions and mechanisms of influence. The panel identified a wide range of social and political factors that affect agricultural systems. The factors were divided into three categories: internal social factors, external social factors and political factors. Factors from each of the three categories were highly ranked, indicating that no single category dominated the others. Although there were contrasting views about the importance of some factors, there was strong consensus about many of them. Globalization and low margins that require increased scale and efficiency were identified as the two most important factors affecting agricultural systems. Several newly emerging factors were identified as well as factors needing further research. A comprehensive understanding of these factors is imperative to help guide scientific research so that beneficial discoveries are accepted and used, and to ensure that policy decisions enhance the future sustainability of agricultural production.

Diversity of different farmer and modern wheat varieties cultivated in contrasting organic farming conditions in Western Europe and implications for European seed and variety legislation

The importance of genetic diversity in cultivated varieties for organic and low-input agriculture has attracted increasing attention in recent years, with a need to identify relevant sources of diversity and strategies for incorporating diversity in plant breeding for organic systems. However, the regulatory system in many countries, particularly in the European Union, restricts the varieties available to farmers to those registered in an official catalogue, and most countries require varieties to go through official tests under conventional management, which has resulted in a lack of suitable varieties available to organic farmers. This study characterized a sample of wheat (Triticum aestivum L.) landraces, historic varieties and varietal mixtures currently of interest to organic farmers in a diverse range of organic conditions on farms in Italy, France and the Netherlands. These varieties were assessed for individual plant and spike characteristics and compared to modern registered wheat varieties grown under the same on-farm conditions. Significant differences in mean values were found among varieties for many plant and spike traits, as well as significant variety-by-environment interactions. There were often similar levels of intra-varietal variability between farmer and modern varieties, indicating that the strong selection for genetic homogeneity to meet regulatory criteria has little impact on the phenotypic variability of certain traits when assessed on-farm. Several farmer varieties had high values of traits related to productivity outside their region of origin, which underlines the need for experimentation with diverse types of varieties in order to find and develop appropriate varieties for organic systems.

How do we address the disconnect between genetic and morphological diversity in germplasm collections

Th e world’s food production systems must keep up with an everincreasing demand in spite of the challenges caused by climate change and environmental degradation. To meet this challenge, plant breeders must have access to genetic diversity for crop improvement. However, genetic homogeneity in the handful of major crops that feed the world limits options for breeding progress ( Swaminathan, 2009 ). Wild and landrace relatives of crop plants provide much needed diversity and are maintained in gene banks worldwide ( McCouch, 2013 ). Th is germplasm resource is underused by breeders, mainly because genotypic and phenotypic data are limited. However, using rapidly developing genomics resources, breeders are unlocking the genetic potential in gene banks and making remarkable advances ( Tanksley and McCouch, 1997 ). Morphological traits and neutral genetic markers are commonly used to characterize germplasm collections, with the goal of improving the value of these collections to breeders ( Brown, 1989 ). Morphological and neutral marker data provide the foundation for the assembly of a core collection, defi ned as a subset of a germplasm collection intended to represent the entire collection. Th e concept of a core collection assumes that the core has some utility for plant improvement. Th at is, the core collection is maximally diverse and is useful for breeding. Evaluating the core collection for key traits should also have some level of predictability for the rest of the collection based on the relatedness of core accessions to other accessions in the collection. It has been recognized for many years that morphological traits do not always provide a good measure of genetic values and may not accurately reveal the genetic variation in a germplasm collection ( Tanksley and McCouch, 1997 ). Consequently, neutral molecular markers have become popular because they are thought to more accurately refl ect genetic relationships in germplasm collections ( Ebana et al., 2008 ). But genetic relatedness measures based on neutral markers may not predict similarity in trait values or parental performance. Th e patterns of allelic variation in a species may be very diff erent for neutral markers compared with genes under selection. Based on a meta-analysis, McKay and Latta (2002) argued that allele frequencies at neutral and selected loci are not correlated because evolutionary forces act diff erently on them. A meta-analysis by Reed and Frankham (2001) showed only weak correlation between neutral molecular markers and quantitative measures of variation. Reeves, Panella, and Richards (2012) found that genetic variation at loci of agronomic interest in core collections assembled using neutral diversity may be lower than in collections assembled at random. In addition, neutral genetic markers identifi ed in single populations or breeding lines may have signifi cant ascertainment bias, which makes them unrepresentative of the full range of functional genetic diversity in the species ( Moragues et al., 2010 ). Our breeding research in potato has revealed a remarkably unexpected result that has led us to question the value of morphological diversity as a proxy for overall genetic diversity. We assessed an F 2 population created by self-pollinating an F 1 clone from a cross between two diploid (2 n = 2 × = 24) potato clones: DM, a completely homozygous clone derived from somatically doubling an androgenic monoploid of a cultivated potato, and M6, a highly inbred clone derived from seven generations of self-pollination of the wild diploid potato relative Solanum chacoense. We evaluated the F 2 population for a variety of morphological features including tuber size, shape, and eye depth; skin and flesh color; and dry matter content. Phenotypic segregation in this F 2 population is astounding ( Fig. 1 ). Th e tuber shape and color variability derived from self-pollinating a single diploid F 1 plant approaches that of the landrace collections maintained in potato genebanks ( Spooner and Hetterscheid, 2005 ) ( Fig. 1 ). 1 Manuscript received 6 May 2015; revision accepted 11 June 2015. 2 USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, 1575 Linden Drive, Madison, Wisconsin; and 3 Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, Wisconsin 53706-1590 USA 4 Author for correspondence: (e-mail: shelley.jansky@ars.usda.gov) doi:10.3732/ajb.1500203 O N T H E N AT U R E O F T H I N G S : E S S AYS

Assessing farmer interest in participatory plant breeding: Who wants to work with scientists?

Participatory research, particularly participatory plant breeding (PPB), can increase the relevance of public-sector research to the agricultural community. PPB has mostly been used in developing countries with resource-poor farmers, but there is increasing interest among farmers in developed countries who are dissatisfied with the performance of available varieties. In 2006, scientists associated with the winter and spring wheat breeding programs in the Department of Crop and Soil Sciences and the Department of Community and Rural Sociology at Washington State University (WSU) conducted a survey of members of the Washington Association of Wheat Growers. Through analysis of the survey results, we sought to understand (1) whether or not farmers want to work with scientists in PPB programs and (2) the determinants of PPB interest. Results indicated that 52% of Washington wheat growers were interested in working with WSU scientists in a participatory breeding program. Interested farmers tended to be younger and college educated with fewer years of farming experience. Moreover, PPB interest appeared to be related positively to farm size, the number of wheat varieties planted, use of and interest in alternative production and marketing practices (e.g., seed saving, organic agriculture), and prior experience with WSU. Based on this analysis and ongoing discussions with farmers, we hope to develop a participatory wheat breeding program where farmers are able to choose their level of involvement with the breeding process based on their interest and needs. This new program will increase the relevance of WSUs wheat breeding programs to farmers in the state and could serve as a model for other public agricultural research programs seeking to increase farmer involvement and, thereby, democratize agricultural research.

Seeds for Organic Agriculture: Development of Participatory Plant Breeding and Farmers’ Networks in France

The lack of seeds and varieties suited to organic agriculture has been a problem for a long time. Conventional breeding strategies do not fit the needs of organic agriculture, which requires specific adaptation to the environment. Moreover, several current breeding methods do not respect the principles of organic agriculture. To overcome these limitations, organic farmers and their organisations initiated participatory plant breeding (PPB) programmes, together with researchers.

Carotenoid Presence Is Associated with the Or Gene in Domesticated Carrot

Ellison et al. provide the first evidence that the genomic region bearing the Or gene is involved in the presence of carotenoids in carrot. Using a global collection of diverse carrot accessions, they identify 12 genomic regions... Carrots are among the richest sources of provitamin A carotenes in the human diet, but genetic variation in the carotenoid pathway does not fully explain the high levels of carotenoids in carrot roots. Using a diverse collection of modern and historic domesticated varieties, and wild carrot accessions, an association analysis for orange pigmentation revealed a significant genomic region that contains the Or gene, advancing it as a candidate for carotenoid presence in carrot. Analysis of sequence variation at the Or locus revealed a nonsynonymous mutation cosegregating with carotenoid content. This mutation was absent in all wild carrot samples and nearly fixed in all orange domesticated samples. Or has been found to control carotenoid presence in other crops but has not previously been described in carrot. Our analysis also allowed us to more completely characterize the genetic structure of carrot, showing that the Western domesticated carrot largely forms one genetic group, despite dramatic phenotypic differences among market classes. Eastern domesticated and wild accessions form a second group, which reflects the recent cultivation history of carrots in Central Asia. Other wild accessions form distinct geographic groups, particularly on the Iberian peninsula and in Northern Africa. Using genome-wide Fst, nucleotide diversity, and the cross-population composite likelihood ratio, we analyzed the genome for regions putatively under selection during domestication and identified 12 regions that were significant for all three methods of detection, one of which includes the Or gene. The Or domestication allele appears to have been selected after the initial domestication of yellow carrots in the East, near the proposed center of domestication in Central Asia. The rapid fixation of the Or domestication allele in almost all orange and nonorange carrots in the West may explain why it has not been found with less genetically diverse mapping populations.