Robert Redden

Phylogeny, phylogeography and genetic diversity of the Pisum genus

The tribe Fabeae (formerly Vicieae) contains some of humanitys most important grain legume crops, namely Lathyrus (grass pea/sweet pea/chickling vetches; about 160 species); Lens (lentils; 4 species); Pisum (peas; 3 species); Vicia (vetches; about 140 species); and the monotypic genus Vavilovia. Reconstructing the phylogenetic relationships within this group is essential for understanding the origin and diversification of these crops. Our study, based on molecular data, has positioned Pisum genetically between Vicia and Lathyrus and shows it to be closely allied to Vavilovia. A study of phylogeography, using a combination of plastid and nuclear markers, suggested that wild pea spread from its centre of origin, the Middle East, eastwards to the Caucasus, Iran and Afghanistan, and westwards to the Mediterranean. To allow for direct data comparison, we utilized model-based Bayesian Analysis of Population structure (BAPS) software on 4429 Pisum accessions from three large world germplasm collections that include both wild and domesticated pea analyzed by retrotransposon-based markers. An analysis of genetic diversity identified separate clusters containing wild material, distinguishing Pisum fulvum, P. elatius and P. abyssinicum, supporting the view of separate species or subspecies. Moreover, accessions of domesticated peas of Afghan, Ethiopian and Chinese origin were distinguished. In addition to revealing the genetic relationships, these results also provided insight into geographical and phylogenetic partitioning of genetic diversity. This study provides the framework for defining global Pisum germplasm diversity as well as suggesting a model for the domestication of the cultivated species. These findings, together with gene-based sequence analysis, show that although introgression from wild species has been common throughout pea domestication, much of the diversity still resides in wild material and could be used further in breeding. Moreover, although existing collections contain over 10,000 pea accessions, effort should be directed towards collecting more wild material in order to preserve the genetic diversity of the species.

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

Economically, legumes (Fabaceae) represent the second most important family of crop plants after the grass family, Poaceae. Grain legumes account for 27% of world crop production and provide 33% of the dietary protein consumed by humans, while pasture and forage legumes provide vital part of animal feed. Fabaceae, the third largest family of flowering plants, has traditionally been divided into the following three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae, all together with 800 genera and 20,000 species. The latter subfamily contains most of the major cultivated food and feed crops. Among the grain legumes are some of mankinds earliest crop plants, whose domestication parallelled that of cereals: Soybean in China; faba bean, lentil, chickpea and pea in the Fertile Crescent of the Near East; cowpeas and bambara groundnut in Africa; soybean and mungbeans in East Asia; pigeonpea and the grams in South Asia; and common bean, lima bean, scarlet runner bean, tepary bean and lupin in Central and South America. The importance of legumes is evidenced by their high representation in ex situ germplasm collections, with more than 1,000,000 accessions worldwide. A detailed knowledge of the phylogenetic relationships of the Fabaceae is essential for understanding the origin and diversification of this economically and ecologically important family of angiosperms. This review aims to combine the phylogenetic and genetic diversity approaches to better illustrate the origin, domestication history and preserved germplasm of major legume crops from 13 genera of six tribes and to indicate further potential both for science and agriculture.

Analysis of a diverse global Pisum sp. collection and comparison to a Chinese local P. sativum collection with microsatellite markers.

Twenty-one informative microsatellite loci were used to assess and compare the genetic diversity among Pisum genotypes sourced from within and outside China. The Chinese germplasm comprised 1243 P. sativum genotypes from 28 provinces and this was compared to 774 P. sativum genotypes that represented a globally diverse germplasm collection, as well as 103 genotypes from related Pisum species. The Chinese P. sativum germplasm was found to contain genotypes genetically distinct from the global gene pool sourced outside China. The Chinese spring type genotypes were separate from the global gene pool and from the other main Chinese gene pool of winter types. The distinct Chinese spring gene pool comprised genotypes from Inner Mongolia and Sha’anxi provinces, with those from Sha’anxi showing the greatest diversity. The other main gene pool within China included both spring types from other northern provinces and winter types from central and southern China, plus some accessions from Inner Mongolia and Sha’anxi. A core collection of Chinese landraces chosen to represent molecular diversity was compared both to the wider Chinese collection and to a geographically diverse core collection of Chinese landraces. The average gene diversity and allelic richness per locus of both the micro-satellite based core and the wider collection were similar, and greater than the geographically diverse core. The genetic diversity of P. sativum within China appears to be quite different to that detected in the global gene pool, including the presence of several rare alleles, and may be a useful source of allelic variation for both major gene and quantitative traits.

Molecular variation among Chinese and global winter faba bean germplasm.

A sample of winter faba bean germplasm from China was compared with germplasm from outside China, using AFLP analyses. Both sets of germplasm were obtained from the National Genebank of China, Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences, Beijing, China. A sample of 39 winter type accessions from outside of China and 204 Chinese landraces and varieties (201 winter types and 3 spring types) were characterized with 10 AFLP primers. These detected 266 polymorphic bands. The Chinese germplasm was clearly separated from the rest of the world in principal component analysis and clustering analysis, with the spring types from China showing the greatest separation. Yunnan germplasm, both landraces and commercial varieties, showed the greatest separation among the germplasm of Chinese winter faba bean provinces. The landraces/varieties from Anhui, Zhejiang, Sichuan, Jianxi, Guizhou and Fujian provinces clustered in a central group.

Evaluation of Helicoverpa and drought resistance in desi and kabuli chickpea

A chickpea collection of 1600 desi and 1400 kabuli were evaluated for yield losses arising from pod borer (Helicoverpa armigera) infestation under rainfed conditions by spraying half the plots to prevent pod borer infestation and allowing the other half to be infested. From these lines, 82 were selected for further detailed evaluation of Helicoverpa resistance and drought resistance under irrigated and rainfed conditions. The yield losses from Helicoverpa damage varied from 10 to 33% depending on the chickpea type and the growing environment. Spreading types were more susceptible to Helicoverpa damage than erect types, as were kabuli types compared to desi types. Yield losses due to Helicoverpa infestation were always greater in the irrigated than in the rainfed materials. Terminal drought reduced yields by 13–37% depending on plant type. The yields in the kabuli chickpea lines were more severely reduced than were the desi types, due to a greater reduction in the number of branches and pods per plant in the kabuli compared to the desi lines. It appears that the extent of pod borer damage varies between the chickpea types, and that desi types have greater drought resistance than kabuli ones. These characteristics should be informative for the population improvement of chickpea for environments in which terminal drought and Helicoverpa damage occur frequently.

Genetic diversity and relationship of global faba bean (Vicia faba L.) germplasm revealed by ISSR markers.

Genetic diversity and relationships of 802 faba bean (Vicia faba L.) landraces and varieties from different geographical locations of China and abroad were examined using ISSR markers. A total of 212 repeatable amplified bands were generated with 11 ISSR primers, of which 209 were polymorphic. Accessions from North China showed highest genetic diversity, while accessions from central China showed low level of diversity. Chinese spring faba bean germplasm was clearly separated from Chinese winter faba bean, based on principal component analysis and UPGMA clustering analysis. Winter accessions from Zhejiang (East China), Jiangxi (East China), Sichuan (Southwest China) and Guizhou (Southwest China) were quite distinct to that from other provinces in China. Great differentiation between Chinese accessions and those from rest of the world was shown with a UPGMA dendrogram. AMOVA analyses demonstrated large variation and differentiation within and among groups of accessions from China. As a continental geographic group, accessions from Europe were genetically closer to those from North Africa. Based on ISSR data, grouping results of accessions from Asia, Europe and Africa were obviously associated with their geographical origin. The overall results indicated that the genetic relationship of faba bean germplasm was closely associated with their geographical origin and their ecological habit.

Large-scale microsatellite development in grasspea (Lathyrus sativus L.), an orphan legume of the arid areas.

BackgroundGrasspea (Lathyrus sativus L., 2n = 14), a member of the family Leguminosae, holds great agronomic potential as grain and forage legume crop in the arid areas for its superb resilience to abiotic stresses such as drought, flood and salinity. The crop could not make much progress through conventional breeding in the past, and there are hardly any detailed molecular biology studies due to paucity of reliable molecular markers representative of the entire genome.ResultsUsing the 454 FLX Titanium pyrosequencing technique, 651,827 simple sequence repeat (SSR) loci were identified and 50,144 nonredundant primer pairs were successfully designed, of which 288 were randomly selected for validation among 23 L. sativus and one L. cicera accessions of diverse provenance. 74 were polymorphic, 70 monomorphic, and 144 with no PCR product. The number of observed alleles ranged from two to five, the observed heterozygosity from 0 to 0.9545, and Shannon’s information index ranged from 0.1013 to 1.0980, respectively. The dendrogram constructed by using unweighted pair group method with arithmetic mean (UPGMA) based on Neis genetic distance, showed obvious distinctions and understandable relationships among the 24 accessions.ConclusionsThe large number of SSR primer pairs developed in this study would make a significant contribution to genomics enabled improvement of grasspea.

Crop wild relatives and climate change

Description based on print version record and CIP data provided by publisher. ; Print version: ; Crop wild relatives and climate change ; Hoboken, New Jersey : Wiley-Blackwell, 2015 ; 9781118854334 ; (DLC) 2015019012. ;

Evidence from Genome-wide Simple Sequence Repeat Markers for a Polyphyletic Origin and Secondary Centers of Genetic Diversity of Brassica juncea in China and India

The oilseed Brassica juncea is an important crop with a long history of cultivation in India and China. Previous studies have suggested a polyphyletic origin of B. juncea and more than one migration from the primary to secondary centers of diversity. We investigated molecular genetic diversity based on 99 simple sequence repeat markers in 119 oilseed B. juncea varieties from China, India, Europe, and Australia to test whether molecular differentiation follows Vavilovs proposal of secondary centers of diversity in India and China. Two distinct groups were identified by markers in the A genome, and the same two groups were confirmed by markers in the B genome. Group 1 included accessions from central and western India, in addition to those from eastern China. Group 2 included accessions from central and western China, as well as those from northern and eastern India. European and Australian accessions were found only in Group 2. Chinese accessions had higher allelic diversity per accession (Group 1) and more private alleles per accession (Groups 1 and 2) than those from India. The marker data and geographic distribution of Groups 1 and 2 were consistent with two independent migrations of B. juncea from its center of origin in the Middle East and neighboring regions along trade routes to western China and northern India, followed by regional adaptation. Group 1 migrated further south and west in India, and further east in China, than Group 2. Group 2 showed diverse agroecological adaptation, with yellow-seeded spring-sown types in central and western China and brown-seeded autumn-sown types in India.

Cool-season grain legume improvement in Australia—use of genetic resources

Abstract. The cool-season grain legume industry in Australia, comprising field pea (Pisum sativum L.), chickpea (Cicer arietinum L.), faba bean (Vicia faba L.), lentil (Lens culinaris ssp. culinaris Medik.), and narrow-leaf lupin (Lupinus angustifolius L.), has emerged in the last 40 years to occupy a significant place in cropping systems. The development of all major grain legume crops—including field pea, which has been grown for over 100 years—has been possible through large amounts of genetic resources acquired and utilised in breeding. Initially, several varieties were released directly from these imports, but the past 25 years of grain legume breeding has recombined traits for adaptation and yield for various growing regions. Many fungal disease threats have been addressed through resistant germplasm, with varying successes. Some threats, e.g. black spot in field pea caused by Mycosphaerella pinodes (Berk. and Blox.) Vestergr., require continued exploration of germplasm and new technology. The arrival of ascochyta blight in chickpea in Australia threatened to destroy the chickpea industry of southern Australia, but thanks to resistant germplasm, it is now on its way to recovery. Many abiotic stresses including drought, heat, salinity, and soil nutritional toxicities continue to challenge the expansion of the grain legume area, but recent research shows that genetic variation in the germplasm may offer new solutions. Just as the availability of genetic resources has been key to successfully addressing many challenges in the past two decades, so it will assist in the future, including adapting to climate change. The acquisition of grain legume germplasm from overseas is a direct result of several Australians who fostered collaborations leading to new collection missions enriching the germplasm base for posterity.