Exploration of the Yield Potential of Mesoamerican Wild Common Beans From Contrasting Eco-Geographic Regions by Nested Recombinant Inbred Populations

Biocultural diversity and crop improvement

Biocultural diversity is the ever-evolving and irreplaceable sum total of all living organisms inhabiting the Earth. It plays a significant role in sustainable productivity and ecosystem services that benefit humanity and is closely allied with human cultural diversity. Despite its essentiality, biodiversity is seriously threatened by the insatiable and inequitable human exploitation of the Earth's resources. One of the benefits of biodiversity is its utilization in crop improvement, including cropping improvement (agronomic cultivation practices) and genetic improvement (plant breeding). Crop improvement has tended to decrease agricultural biodiversity since the origins of agriculture, but awareness of this situation can reverse this negative trend. Cropping improvement can strive to use more diverse cultivars and a broader complement of crops on farms and in landscapes. It can also focus on underutilized crops, including legumes. Genetic improvement can access a broader range of biodiversity sources and, with the assistance of modern breeding tools like genomics, can facilitate the introduction of additional characteristics that improve yield, mitigate environmental stresses, and restore, at least partially, lost crop biodiversity. The current legal framework covering biodiversity includes national intellectual property and international treaty instruments, which have tended to limit access and innovation to biodiversity. A global system of access and benefit sharing, encompassing digital sequence information, would benefit humanity but remains an elusive goal. The Kunming-Montréal Global Biodiversity Framework sets forth an ambitious set of targets and goals to be accomplished by 2030 and 2050, respectively, to protect and restore biocultural diversity, including agrobiodiversity.

Identification of quantitative trait loci for drought tolerance in Bukoba/Kijivu Andean mapping population of common bean

KEY MESSAGE

Quantitative Trait Loci "hotspots" for drought tolerance were identified on chromosomes Pv06, Pv07 and Pv10 of common bean. Drought is a major production constraint of common bean (Phaseolus vulgaris L.) worldwide. The objective of this study was to identify the Quantitative Trait Loci (QTL) for drought tolerance in an Andean population of Recombinant Inbred Lines (RILs). A total of 155 F5:7 RILs derived from a cross between Kijivu (drought tolerant) and Bukoba (drought susceptible) were evaluated for drought tolerance in field and pot experiments. Four field experiments were conducted at three locations in Zambia in 2020 and 2021. All field trials were conducted in the dry season under irrigation. The 155 RILs were genotyped with 11,292 SNPs, and composite interval mapping was conducted to identify QTL for drought tolerance. Seed yield for Kijivu under drought stress was consistently higher than for Bukoba across all four field trials. A total of 60 QTL were identified for morphological, agronomic, and physiological traits under drought stress and non-stress conditions. However, the majority of these QTL were specific to drought stress. QTL "hotspots" for drought tolerance were identified on chromosomes Pv06, Pv07, and Pv10. Extensive co-localizations for agronomic and morpho-physiological traits under drought stress were observed at the three drought-tolerance QTL hotspots. Additionally, these three QTL hotspots overlapped with previously identified QTL for drought tolerance, while several others identified QTL are novel. The three identified QTL hotspots could be used in future marker-assisted selection for drought tolerance in common bean.

Hyperspectral Remote Sensing for Phenotyping the Physiological Drought Response of Common and Tepary Bean

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.

Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies

Global agricultural industries are under pressure to meet the future food demand; however, the existing crop genetic diversity might not be sufficient to meet this expectation. Advances in genome sequencing technologies and availability of reference genomes for over 300 plant species reveals the hidden genetic diversity in crop wild relatives (CWRs), which could have significant impacts in crop improvement. There are many ex-situ and in-situ resources around the world holding rare and valuable wild species, of which many carry agronomically important traits and it is crucial for users to be aware of their availability. Here we aim to explore the available ex-/in- situ resources such as genebanks, botanical gardens, national parks, conservation hotspots and inventories holding CWR accessions. In addition we highlight the advances in availability and use of CWR genomic resources, such as their contribution in pangenome construction and introducing novel genes into crops. We also discuss the potential and challenges of modern breeding experimental approaches (e.g. de novo domestication, genome editing and speed breeding) used in CWRs and the use of computational (e.g. machine learning) approaches that could speed up utilization of CWR species in breeding programs towards crop adaptability and yield improvement.

Genetic dissection of morphological variation in rosette leaves and leafy heads in cabbage (Brassica oleracea var. capitata)

Correlations between morphological traits of cabbage rosette leaves and heads were found. Genome-wide association studies of these traits identified 50 robust quantitative trait loci in multiple years. Half of these loci affect both organs. Cabbage (Brassica oleracea var. capitata) is an economically important vegetable crop cultivated worldwide. Cabbage plants go through four vegetative stages: seedling, rosette, folding and heading. Rosette leaves are the largest leaves of cabbage plants and provide most of the energy needed to produce the leafy head. To understand the relationship and the genetic basis of leaf development and leafy head formation, 308 cabbage accessions were scored for rosette leaf and head traits in three-year field trials. Significant correlations were found between morphological traits of rosette leaves and heads, namely leaf area with the head area, height and width, and leaf width with the head area and head height, when heads were harvested at a fixed number of days after sowing. Fifty robust quantitative trait loci (QTLs) for rosette leaf and head traits distributed over all nine chromosomes were identified with genome-wide association studies. All these 50 loci were identified in multiple years and generally affect multiple traits. Twenty-five of the QTL were associated with both rosette leaf and leafy head traits. We discuss thirteen candidate genes identified in these QTL that are expressed in heading leaves, with an annotation related to auxin and other phytohormones, leaf development, and leaf polarity that likely play a role in leafy head development or rosette leaf expansion.

Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean

The population growth trend in recent decades has resulted in continuing efforts to guarantee food security in which leguminous plants, such as the common bean (Phaseolus vulgaris L.), play a particularly important role as they are relatively cheap and have high nutritional value. To meet this demand for food, the main target for genetic improvement programs is to increase productivity, which is a complex quantitative trait influenced by many component traits. This research aims to identify Quantitative Trait Nucleotides (QTNs) associated with productivity and its components using multi-locus genome-wide association studies. Ten morpho-agronomic traits [plant height (PH), first pod insertion height (FPIH), number of nodules (NN), pod length (PL), total number of pods per plant (NPP), number of locules per pod (LP), number of seeds per pod (SP), total seed weight per plant (TSW), 100-seed weight (W100), and grain yield (YLD)] were evaluated in four environments for 178 Mesoamerican common bean domesticated accessions belonging to the Brazilian Diversity Panel. In order to identify stable QTNs, only those identified by multiple methods (mrMLM, FASTmrMLM, pLARmEB, and ISIS EM-BLASSO) or in multiple environments were selected. Among the identified QTNs, 64 were detected at least thrice by different methods or in different environments, and 39 showed significant phenotypic differences between their corresponding alleles. The alleles that positively increased the corresponding traits, except PH (for which lower values are desired), were considered favorable alleles. The most influenced trait by the accumulation of favorable alleles was PH, showing a 51.7% reduction, while NN, TSW, YLD, FPIH, and NPP increased between 18 and 34%. Identifying QTNs in several environments (four environments and overall adjusted mean) and by multiple methods reinforces the reliability of the associations obtained and the importance of conducting these studies in multiple environments. Using these QTNs through molecular techniques for genetic improvement, such as marker-assisted selection or genomic selection, can be a strategy to increase common bean production.

Phaseolus vulgaris MIR1511 genotypic variations differentially regulate plant tolerance to aluminum toxicity

The common-bean (Phaseolus vulgaris), a widely consumed legume, originated in Mesoamerica and expanded to South America, resulting in the development of two geographically distinct gene pools. Poor soil condition, including metal toxicity, are often constraints to common-bean crop production. Several P. vulgaris miRNAs, including miR1511, respond to metal toxicity. The MIR1511 gene sequence from the two P. vulgaris model sequenced genotypes revealed that, as opposed to BAT93 (Mesoamerican), the G19833 (Andean) accession displays a 58-bp deletion, comprising the mature and star miR1511 sequences. Genotyping-By-Sequencing data analysis from 87 non-admixed Phaseolus genotypes, comprising different Phaseolus species and P. vulgaris populations, revealed that all the P. vulgaris Andean genotypes and part of the Mesoamerican (MW1) genotypes analyzed displayed a truncated MIR1511 gene. The geographic origin of genotypes with a complete versus truncated MIR1511 showed a distinct distribution. The P. vulgaris ALS3 (Aluminum Sensitive Protein 3) gene, known to be important for aluminum detoxification in several plants, was experimentally validated as the miR1511 target. Roots from BAT93 plants showed decreased miR1511 and increased ALS3 transcript levels at early stages under aluminum toxicity (AlT), while G19833 plants, lacking mature miR1511, showed higher and earlier ALS3 response. Root architecture analyses evidenced higher tolerance of G19833 plants to AlT. However, G19833 plants engineered for miR1511 overexpression showed lower ALS3 transcript level and increased sensitivity to AlT. Absence of miR1511 in Andean genotypes, resulting in a diminished ALS3 transcript degradation, appears to be an evolutionary advantage to high Al levels in soils with increased drought conditions.

Introgression Breeding in Cowpea [Vigna unguiculata (L.) Walp.]

The narrow base of genetic diversity characteristic of cowpea can be attributed to it being self-pollinating, evolving from narrow wild germplasm and exhibiting very limited gene flow between wild and cultivated types. Backcrossing to introduce simply inherited desirable traits and utilization of improved breeding lines and varieties as parents in crossing programs further narrowed the genetic base of cowpea varieties. In most cowpea breeding programs, genes for resistance and market traits were pyramided into lines characterized by high levels of acceptance to farmers and consumers. Besides predisposing widely distributed improved varieties to genetic vulnerability, a narrow base of genetic variation may be contributing to the plateauing in cowpea grain yield, which compromises genetic gains. Cross compatible wild relatives have not been used in variety development because breeders shy away from them due to their tiny seed size, unattractive seed coat color and texture, pod shattering, and susceptibility to viruses. A number of wild cowpea relatives, both within and outside section Catiang of Vigna species, have been evaluated for their reaction to cowpea insect pests and diseases. Vigna vexillata lines were resistant to the legume pod borer (Maruca vitrata), the cowpea weevil (Callosobruchus maculatus), and Striga gesnerioides but are cross incompatible with cultivated cowpea. Some lines among the cross compatible wild relative V. unguiculata ssp. dekindtiana were found to be resistant to aphid in the seedling stage, while others showed good levels of drought and heat tolerance. Molecular markers are being generated to identify quantitative trait loci (QTL) with effects on some desirable attributes in cowpea. Modern breeding tools, including transgenics, can be applied for the improvement of cowpea, bypassing the natural barriers of traditional breeding. Transgenic cowpea with Bt gene cry1Ab showing resistance to M. vitrata has been released in Nigeria. Genome editing, a powerful emerging tool, can also be used for developing improved cowpea varieties with durable resistance to pests and diseases.