A reduction in pod shattering is one of the main components of grain legume domestication. Despite this, many domesticated legumes suffer serious yield losses due to shattering, particularly under arid conditions. Mutations related to pod shattering modify the twisting force of pod walls or the structural strength of the dehiscence zone in pod sutures. At a molecular level, a growing body of evidence indicates that these changes are controlled by a relatively small number of key genes that have been selected in parallel across grain legume species, supporting partial molecular convergence. Legume homologs of Arabidopsis thaliana silique shattering genes play only minor roles in legume pod shattering. Most domesticated grain legume species contain multiple shattering-resistance genes, with mutants of each gene typically showing only partial shattering resistance. Hence, crosses between varieties with different genes lead to transgressive segregation of shattering alleles, producing plants with either enhanced shattering resistance or atavistic susceptibility to the trait. The frequency of these resistance pod-shattering alleles is often positively correlated with environmental aridity. The continued development of pod-shattering-related functional information will be vital for breeding crops that are suited to the increasingly arid conditions expected in the coming decades.

Pod quality and yield traits in snap bean (Phaseolus vulgaris L.) influence consumer preferences, crop adoption by farmers, and the ability of the product to be commercially competitive locally and globally. The objective of the study was to identify the quantitative trait loci (QTL) for pod quality and yield traits in a snap × dry bean recombinant inbred line (RIL) population. A total of 184 F6 RILs derived from a cross between Vanilla (snap bean) and MCM5001 (dry bean) were grown in three field sites in Kenya and one greenhouse environment in Davis, CA, USA. They were genotyped at 5,951 single nucleotide polymorphisms (SNPs), and composite interval mapping was conducted to identify QTL for 16 pod quality and yield traits, including pod wall fiber, pod string, pod size, and harvest metrics. A combined total of 44 QTL were identified in field and greenhouse trials. The QTL for pod quality were identified on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, and Pv07, and for pod yield were identified on Pv08. Co-localization of QTL was observed for pod quality and yield traits. Some identified QTL overlapped with previously mapped QTL for pod quality and yield traits, with several others identified as novel. The identified QTL can be used in future marker-assisted selection in snap bean.

Significance: Plant domestication has radically modified crop morphology and development. Nevertheless, many crops continue to display some atavistic characteristics that were advantageous to their wild ancestors, such as pod dehiscence (PD). Domesticated common bean (Phaseolus vulgaris), a nutritional staple for millions of people globally, shows considerable variation in PD. Here, we identified multiple genetic regions controlling PD in common bean grown throughout geographically distributed lineages. For example, on chromosome Pv03, PvPdh1 shows a single base-pair substitution that is strongly associated with decreased PD and expansion of the crop into northern Mexico, where the arid conditions promote PD. The environmental dependency and genetic redundancy explain the maintenance of atavistic traits under domestication. Knowledge of PD genetics will assist in developing aridity-adapted varieties. A reduction in pod dehiscence (PD) is an important part of the domestication syndrome in legumes, including common bean. Despite this, many modern dry bean varieties continue to suffer yield reductions due to dehiscence, an atavistic trait, which is particularly problematic in hot, dry environments. To date, the genetic control of this important trait has been only partially resolved. Using QTL mapping and GWAS, we identified major PD QTLs in dry beans on chromosomes Pv03, Pv05, Pv08, and Pv09, three of which had not been described previously. We further determined that the QTL on chromosome Pv03, which is strongly associated with PD in Middle American beans, includes a dirigent-like candidate gene orthologous to Pod dehiscence 1 (Pdh1) of soybean. In this gene, we identified a substitution in a highly conserved amino acid that is unique to PD-resistant varieties. This allele is associated with the expansion of Middle American domesticated common beans into the arid environments of northern Mexico, resulting in a high allelic frequency in the domesticated ecogeographic race Durango. The polygenic redundancy and environmental dependency of PD resistance may explain the maintenance of this atavistic characteristic after domestication. Use of these alleles in breeding will reduce yield losses in arid growing conditions, which are predicted to become more widespread in coming decades.

Plant domestication has strongly modified crop morphology and development. Nevertheless, many crops continue to display atavistic characteristics that were advantageous to their wild ancestors but are deleterious under cultivation, such as pod dehiscence (PD). Here, we provide the first comprehensive assessment of the inheritance of PD in the common bean (Phaseolus vulgaris), a major domesticated grain legume. Using three methods to evaluate the PD phenotype, we identified multiple, unlinked genetic regions controlling PD in a biparental population and two diversity panels. Subsequently, we assessed patterns of orthology among these loci and those controlling the trait in other species. Our results show that different genes were selected in each domestication and ecogeographic race. A chromosome Pv03 dirigent-like gene, involved in lignin biosynthesis, showed a base-pair substitution that is associated with decreased PD. This haplotype may underlie the expansion of Mesoamerican domesticates into northern Mexico, where arid conditions promote PD. The rise in frequency of the decreased-PD haplotype may be a consequence of the markedly different fitness landscape imposed by domestication. Environmental dependency and genetic redundancy can explain the maintenance of atavistic traits under domestication.

Key message

A common bean shattering-resistance allele of PvPdh1 reduces pod twists during dehiscence, shows dominance that varies by phenotyping method, is part of a selective sweep, and can be introgressed using CAPS markers. Some varieties of common bean (Phaseolus vulgaris L.) suffer from pod shattering, which can severely reduce yields, especially in arid conditions. The PvPdh1 locus on chromosome Pv03 has recently been described as a major locus controlling pod shattering in common bean and could be used to mitigate pod shattering in the future. Despite this, the role of a possible second locus on chromosome Pv08 remains unclear and patterns of dominance and epistasis between alleles of these genes have not been resolved. This information will be vital for efficient selection to decrease pod shattering. Further, the genetic diversity around the PvPdh1 gene has not yet been thoroughly explored, and there are not yet genetic screens that can be used to evaluate pod shattering in segregating populations. Here, we have developed a recombinant inbred population to determine the roles of genes implicated in pod shattering and evaluate the patterns of dominance among the relevant alleles. Our results suggest that a PvPdh1 allele reduces pod valve twisting, and its dominance varies by phenotyping method. This allele is the only genetic variant that provides environmentally stable and widespread resistance to pod shattering in Middle American common beans grown for grain. Further analyses identified a selective sweep around PvPdh1 with greater nucleotide diversity in individuals with the ancestral, shattering-susceptible allele. Finally, we developed simple, effective CAPS markers to facilitate the introgression of PvPdh1 into new varieties of common bean. These genetic resources will be critical for improving the aridity resilience of a major global staple.

Anthracnose caused by Colletotrichum lindemuthianum is a major disease of common bean (Phaseolus vulgaris) worldwide. Yellow beans are a major market class of common bean especially in eastern and southern Africa. The Yellow Bean Collection (YBC), which is comprised of 255 genotypes, and has not been used previously in genetic studies on anthracnose, is an excellent genetic resource for understanding the extent of anthracnose resistance and its genetic architecture in the yellow bean market class. The objectives of this study were i) evaluate the YBC for resistance to races 5, 19, 39, 51, 81, 183, 1050 and 1105 of C. lindemuthianum. and ii) conduct genome-wide association analysis to identify genomic regions and candidate genes associated with resistance to C. lindemuthianum. The YBC was genotyped with 72,866 SNPs, and genome-wide association analysis was conducted using Mixed Linear Model in TASSEL. Andean and Middle American genotypes with superior levels of resistance to the eight races were identified. YBC278 was the only one among 255 genotypes that was highly resistant to all eight races. Resistance to anthracnose in the YBC was controlled by major-effect loci on chromosomes Pv01, Pv03, Pv04, Pv05 and Pv07. The genomic region on Pv01, which overlapped with the Andean locus Co-1 provided resistance to races 81, 1050 and 1105. Significant SNPs for resistance to race 39 were identified on Pv02. The genomic region on Pv04, which overlapped with known major-effect loci Co-3, Co-15, Co-16, Co-y and Co-z, provided resistance to races 5, 19, 51 and 183. Novel genomic regions for resistance to race 39 were identified on Pv05 and Pv07. Plant resistance genes (R genes) with NB-ARC and LRR domains, which occurred in clusters, were identified as positional candidate genes for genomic regions on Pv02 and Pv04.

Proximal remote sensing offers a powerful tool for high-throughput phenotyping of plants for assessing stress response. Bean plants, an important legume for human consumption, are often grown in regions with limited rainfall and irrigation and are therefore bred to further enhance drought tolerance. We assessed physiological (stomatal conductance and predawn and midday leaf water potential) and ground- and tower-based hyperspectral remote sensing (400 to 2,400 nm and 400 to 900 nm, respectively) measurements to evaluate drought response in 12 common bean and 4 tepary bean genotypes across 3 field campaigns (1 predrought and 2 post-drought). Hyperspectral data in partial least squares regression models predicted these physiological traits (R ² = 0.20 to 0.55; root mean square percent error 16% to 31%). Furthermore, ground-based partial least squares regression models successfully ranked genotypic drought responses similar to the physiologically based ranks. This study demonstrates applications of high-resolution hyperspectral remote sensing for predicting plant traits and phenotyping drought response across genotypes for vegetation monitoring and breeding population screening.

The vulnerability of cyber-physical systems to cyber attack is well known, and the requirement to build cyber resilience into these systems has been firmly established. The key challenge this paper addresses is that maturing this discipline requires the development of techniques, tools, and processes for objectively, rigorously, and quantitatively measuring the attributes of cyber resilience. Researchers and program managers need to be able to determine if the implementation of a resilience solution actually increases the resilience of the system. In previous work, a table top exercise was conducted using a notional heavy vehicle on a fictitious military mission while under a cyber attack. While this exercise provided some useful data, more and higher fidelity data is required to refine the measurement methodology. This paper details the efforts made to construct a cost-effective experimentation infrastructure to provide such data. It also presents a case study using some of the data generated by the infrastructure.

This manuscript reviews two decades of projects funded by the Kirkhouse Trust (KT), a charity registered in the UK. KT was established to improve the productivity of legume crops important in African countries and in India. KTs requirements for support are: (1) the research must be conducted by national scientists in their home institution, either a publicly funded agricultural research institute or a university; (2) the projects need to include a molecular biology component, which to date has mostly comprised the use of molecular markers for the selection of one or more target traits in a crop improvement programme; (3) the projects funded are included in consortia, to foster the creation of scientific communities and the sharing of knowledge and breeding resources. This account relates to the key achievements and challenges, reflects on the lessons learned and outlines future research priorities.

Sweetpotatoes are a major crop in California, ranking sixth in value among organic commodities in the state. In recent years, there has been growing consumer interest in diverse specialty varieties, particularly purple types and those associated with Asian American and Pacific Islander (AAPI) communities, some of which are currently imported into the state. In this study, we screened 45 diverse sweetpotato varieties and breeding lines under California organic conditions in a preliminary characterization of their agronomic performance. We then conducted culinary evaluations with a tasting panel of students primarily identifying as Asian/Asian American to determine the preference for each type in terms of flavor and culinary appeal. Our results indicated that major tradeoffs exist among existing germplasm, with no variety or line excelling across all agronomic and culinary traits. These results suggest that sweetpotato breeding could be an effective mechanism to combine superior agronomic traits of major commercial classes with the high culinary quality of diverse materials that are not adapted to California organic production. These results provide a strong justification for the value of sweetpotato breeding to ultimately promote a more profitable, sustainable, and just food system in the region.