Male sterility in beans (Phaseolus vulgaris L.)

Rheenen, H. A. van; Muigai, S. G. S.; Kitivo, D. K.

doi:10.1007/bf00038946

Cited by 9 publications

(6 citation statements)

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“…Beyond C9ORF72, our pleiotropy analyses detected novel genetic signal within numerous loci including GIPC1, ELMO1 and COL16A and confirmed previously reported variants, such as ATXN2, KIF5A, UNC13A and MOBP 4-6 . Neither as polygenic as schizophrenia 18 or Alzheimer's disease 19 nor purely oligogenic 5 , it is likely that the genetic architecture of ALS is a continuum of common low-risk variants and rare high-risk variants.…”

Section: Discussionmentioning

confidence: 99%

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Partitioning the genetic architecture of amyotrophic lateral sclerosis

Broce

Fan

Olney

et al. 2018

Preprint

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The genetic basis of sporadic amyotrophic lateral sclerosis (ALS) is not well understood. Using large genome-wide association studies and validated tools to quantify genetic overlap, we systematically identified single nucleotide polymorphisms (SNPs) associated with ALS conditional on genetic data from 65 different traits and diseases from >3 million people. We found strong genetic enrichment between ALS and a number of disparate traits including frontotemporal dementia, coronary artery disease, C-reactive protein, celiac disease and memory function. Beyond C9ORF72, we detected novel genetic signal within numerous loci including GIPC1, ELMO1 and COL16A and confirmed previously reported variants, such as ATXN2, KIF5A, UNC13A and MOBP. We found that ALS variants form a small-world co-expression network characterized by highly inter-connected 'hub' genes. This network clustered into smaller sub-networks, each associated with a unique function. Altered gene expression of several subnetworks and hubs was over-represented in neuropathological samples from ALS patients and SOD1 G93A mice. Our collective findings indicate that the genetic architecture of ALS can be partitioned into distinct components where some genes are highly important for developing disease. These findings have implications for stratification and enrichment strategies for ALS clinical trials. Properties of the ALS biological networksWe assessed the network structure of the physical protein-protein interaction network, coexpression network, and genetic interactions network. Specifically, we asked whether some genes play a more influential role than others. Most complex networks have a small-world property characterized by relatively short paths between any pair of nodes (genes) 15 . In smallworld networks, perturbing any given node is thought to also perturb neighboring nodes and the entire network in general. Quantitatively, a network is considered small-world if its "smallworldness" index is higher than one (a stricter rule is small-worldness >=3) 16 . Further, the clustering coefficient for the target small-world network should be higher than the clustering coefficient of a comparable random network. Also, the average shortest path length of the target network should be similar or higher (but not substantially higher) than a comparable random network.7 First, we evaluated the degree to which each network assumed a small-work network structure. The co-expression interaction network consisted of 95 nodes and 132 edges, had a small-world index of 6.06, a diameter of 13, and average shortest path length of 5.12. The clustering coefficient was 0.102, which is higher than the clustering coefficient of a random graph with the same number of indices (0.031). The physical protein-protein interaction network consisted of 85 nodes and 41 edges, had a small-world index of 4.43, a diameter of 5, and average shortest path length of 82.03. The clustering coefficient was 0.326, which is also higher than the clustering coefficient of a random network with the same ...

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Section: Discussionmentioning

confidence: 99%

“…Prior work suggests that sporadic ALS is genetically characterized by a few rare variants, each explaining a substantial portion of the inherited risk (oligogenic) [2][3][4] . However, more recent evidence indicates that low-risk, common variants underlie ALS (polygenic) 5 .…”

Section: Introductionmentioning

confidence: 99%

Partitioning the genetic architecture of amyotrophic lateral sclerosis

Broce

Fan

Olney

et al. 2018

Preprint

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“…Only few domesticated and wild forms of Phaseolus vulgaris are sexually compatible and in some Andean and Mesoamerican parents F 1 hybrid weakness is found. These hybridization barriers are due to the presence of incompatibility genes in some Mesoamerican (Dl1) and Andean (Dl2) wild and domesticated populations (van Reheenen et al 1979 ;Shii et al 1980 ;Singh and Gutierrez 1984 ;Vieira et al 1989 ). These genes lead to inviable F 1 hybrids (Shii et al 1980 ;Gepts and Bliss 1985 ) and hybrid weakness and phenotypic abnormalities in later generations (Koinange and Gepts 1992 ;Debouck et al 1993 ;Freyre et al 1996 ;Singh and Molina 1996 ).…”

Section: Primary Gene Poolmentioning

confidence: 97%

“…The occurrence of abnormal F 1 weakness or dwarfi sm within P. vulgaris crosses have been reviewed (Gepts and Bliss 1985 ;Singh and Gutierrez 1984 ). Shii et al ( 1980 ) and van Reheenen et al ( 1979 ) reported that F 1 abnormality was controlled by two complementary dominant genes which suppress the growth and root development. The allelic dosage of Dl1 in the root and Dl2 in the shoot rather than the genotype of the whole plant determines the severity of expression.…”

Section: Barriers To Interspecifi C Hybridizationmentioning

confidence: 98%

Common Bean

Pathania¹,

Sharma²

2014

Broadening the Genetic Base of Grain Legumes

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The chapter on the common bean reviews the origin and domestication, gene pool organization and their evolutionary relationship, genetic diversity and gene fl ow assessment, production constraints, crop productionlimiting factors, and crop improvement strategies. While the common bean originated in the Americas, it is now widely grown in all continents of the world. Several bean germplasm banks have been established and contain diverse genetic resources comprising fi ve domesticated and wild Phaseolus species, as well as an incipient stock collection. Unique among crop plants, the common bean consists of two geographically distinct evolutionary lineages that predate domestication and trace back to a common, still extant ancestor. The common bean cultivated across the world comprises of two major gene pools: the Andean originating from the Andes mountains of South America and the Mesoamerican from Mexico and Central America along with well-established races. Gene fl ow between domesticated and wild beans led to substantial introgression of alleles from the domesticated gene pool into the wild gene pool and vice versa. Like other crops, the common bean also suffers from various biotic and abiotic stresses; however, these constraints vary with the agroecological regions experiencing tropical to temperate environments. The important biotic and abiotic constraints limiting bean production are bean anthracnose, angular leaf spot, bean common mosaic and necrosis virus, bean golden mosaic virus, bacterial blights, drought, and phosphorus defi ciency. The common bean improvement program in Europe and the USA is mainly focused on biotic and abiotic factors, mainly diseases, drought, and biofortifi cation involving intra-and interspecifi c hybridization programs.

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“…The wild forms of the former two have limited gene flow [Zoro Bi et al (2003); Rendón-Anaya et al (2017), respectively]. As additional mechanisms that promote outcrossing, one should mention that a couple of common bean plants with cytoplasmic male sterility in fertile accessions are known (Mackenzie, 1991), as well as male sterile plants due to recessive genes (van Rheenen et al, 1979;Mutschler and Bliss, 1980). Tepary bean is cleistogamous (Waines and Barnhart, 2001), and possibly the other species with very small flowers [e.g., P. macvaughii, P. microcarpus Mart.].…”

Section: Section 1: Biological Bases Of Gene Flow In the Genus Phaseolusmentioning

confidence: 99%

Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens

et al. 2021

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The genus Phaseolus, native to the Americas, is composed of more than eighty wild species, five of which were domesticated in pre-Columbian times. Since the beginning of domestication events in this genus, ample opportunities for gene flow with wild relatives have existed. The present work reviews the extent of gene flow in the genus Phaseolus in primary and secondary areas of domestication with the aim of illustrating how this evolutionary force may have conditioned ecological fitness and the widespread adoption of cultigens. We focus on the biological bases of gene flow in the genus Phaseolus from a spatial and time perspective, the dynamics of wild-weedy-crop complexes in the common bean and the Lima bean, the two most important domesticated species of the genus, and the usefulness of genomic tools to detect inter and intraspecific introgression events. In this review we discuss the reproductive strategies of several Phaseolus species, the factors that may favor outcrossing rates and evidence suggesting that interspecific gene flow may increase ecological fitness of wild populations. We also show that wild-weedy-crop complexes generate genetic diversity over which farmers are able to select and expand their cultigens outside primary areas of domestication. Ultimately, we argue that more studies are needed on the reproductive biology of the genus Phaseolus since for most species breeding systems are largely unknown. We also argue that there is an urgent need to preserve wild-weedy-crop complexes and characterize the genetic diversity generated by them, in particular the genome-wide effects of introgressions and their value for breeding programs. Recent technological advances in genomics, coupled with agronomic characterizations, may make a large contribution.

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Male sterility in beans (Phaseolus vulgaris L.)

Cited by 9 publications

References 0 publications

Partitioning the genetic architecture of amyotrophic lateral sclerosis

Partitioning the genetic architecture of amyotrophic lateral sclerosis

Common Bean

Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens

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