skip to main content

Title: Allometry and volumes in a nutshell: Analyzing walnut morphology using three‐dimensional X‐ray computed tomography

Persian walnuts (Juglans regiaL.) are the second most produced and consumed tree nut, with over 2.6 million metric tons produced in the 2022–2023 harvest cycle alone. The United States is the second largest producer, accounting for 25% of the total global supply. Nonetheless, producers face an ever‐growing demand in a more uncertain climate landscape, which requires effective and efficient walnut selection and breeding of new cultivars with increased kernel content and easy‐to‐open shells. Past and current efforts select for these traits using hand‐held calipers and eye‐based evaluations. Yet there is plenty of morphology that meets the eye but goes unmeasured, such as the volume of inner air or the convexity of the kernel. Here, we study the shape of walnut fruits based on X‐ray computed tomography three‐dimensional reconstructions. We compute 49 different morphological phenotypes for 1264 individual nuts comprising 149 accessions. These phenotypes are complemented by traits of breeding interest such as ease of kernel removal and kernel‐to‐nut weight ratio. Through allometric relationships, relative growth of one tissue to another, we identify possible biophysical constraints at play during development. We explore multiple correlations between all morphological and commercial traits and identify which morphological traits can explain the most variability of commercial traits. We show that using only volume‐ and thickness‐based traits, especially inner air content, we can successfully encode several of the commercial traits.

more » « less
Award ID(s):
2106578 2310355
Author(s) / Creator(s):
 ;  ;  ;  ;  
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
The Plant Phenome Journal
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Eastern black walnut (Juglans nigraL.), one of the most valuable timber and veneer trees in North America, provides nut shells with unique industrial uses and nut kernels with distinctive culinary attributes. A mature F1full-sib progeny orchard of 248 individuals from the cross of two eastern black walnut cultivars provides a long-term resource for discovering genetic mechanisms controlling life history, quality traits, and stress resistance. The genetic linkage map, constructed with 356 single nucleotide polymorphism (SNP) markers and 62 expressed sequence tag simple sequence repeats (EST-SSRs), is 1645.7 cM in length, distributed across the expected 16 linkage groups. In this first application of QTL mapping inJ. nigra, we report QTL for budbreak, peak pistillate bloom, peak staminate bloom, and heterodichogamy. A dominant major QTL for heterodichogamy is reported, the sequence for which is syntenic with the heterodichogamy QTL on chromosome 11 of Persian walnut (J. regiaL.). The mapping population parents are both protogynous, and segregation suggests a Mendelian component, with a 3:1-like inheritance pattern from heterozygous parents. Mapping the sequenced EST-SSR markers to theJ. regia“Chandler” V2.0 genome sequence revealed evidence for collinearity and structural changes on two of the sixteen chromosomes. The inclusion of sequenced EST-SSR markers enables the direct comparison of this and subsequentJ. nigramaps and otherJuglandaceaegenetic maps. This investigation initiates long-term QTL detection studies for quality and stress resistance traits in black walnut.

    more » « less
  2. Dreisigacker, Susanne (Ed.)
    Abstract Over the past century of maize (Zea mays L.) breeding, grain yield progress has been the result of improvements in several other intrinsic physiological and morphological traits. In this study, we describe (i) the contribution of kernel weight (KW) to yield genetic gain across multiple agronomic settings and breeding programs, and (ii) the physiological bases for improvements in KW for US hybrids. A global-scale literature review concludes that rates of KW improvement in US hybrids were similar to those of other commercial breeding programs but extended over a longer period of time. There is room for a continued increase of kernel size in maize for most of the genetic materials analysed, but the trade-off between kernel number and KW poses a challenge for future yield progress. Through phenotypic characterization of Pioneer Hi-Bred ERA hybrids in the USA, we determine that improvements in KW have been predominantly related to an extended kernel-filling duration. Likewise, crop improvement has conferred on modern hybrids greater KW plasticity, expressed as a better ability to respond to changes in assimilate availability. Our analysis of past trends and current state of development helps to identify candidate targets for future improvements in maize. 
    more » « less
  3. Premise of the Study

    The key to increased cassava production is balancing the trade‐off between marketable roots and traits that drive nutrient and water uptake. However, only a small number of protocols have been developed for cassava roots. Here, we introduce a set of new variables and methods to phenotype cassava roots and enhance breeding pipelines.


    Different cassava genotypes were planted in pot and field conditions under well‐watered and drought treatments. We developed cassava shovelomics and used digital imaging of root traits (DIRT) to evaluate geometrical root traits in addition to common traits (e.g., length, number).


    Cassava shovelomics andDIRTwere successfully implemented to extract root phenotypes, and a large phenotypic variation for root traits was observed. Significant correlations were found among root traits measured manually and byDIRT. Drought significantly decreased shoot dry weight, total root number, and root length by 84%, 30%, and 25%, respectively. High adventitious root number was associated with increased shoot dry weight (r= 0.44) under drought.


    Our methods allow for high‐throughput cassava root phenotyping, which makes a breeding program targeting root traits feasible. We suggest that root number is a breeding target for improved cassava production under drought.

    more » « less
  4. Abstract

    Doubled haploids (DHs) are an important breeding tool for creating maize inbred lines. One bottleneck in the DH process is the manual separation of haploids from among the much larger pool of hybrid siblings in a haploid induction cross. Here, we demonstrate the ability of single‐kernel near‐infrared reflectance spectroscopy (skNIR) to identify haploid kernels. The skNIR is a high‐throughput device that acquires an NIR spectrum to predict individual kernel traits. We collected skNIR data from haploid and hybrid kernels in 15 haploid induction crosses and found significant differences in multiple traits such as percent oil, seed weight, or volume, within each cross. The two kernel classes were separated by their NIR profile using Partial Least Squares Linear Discriminant Analysis (PLS‐LDA). A general classification model, in which all induction crosses were used in the discrimination model, and a specific model, in which only kernels within a specific induction cross, were compared. Specific models outperformed the general model and were able to enrich a haploid selection pool to above 50% haploids. Applications for the instrument are discussed.

    more » « less
  5. Abstract

    Age and environment are important determinants of reproductive parameters in long‐lived organisms. These factors may interact to determine breeding responses to environmental change, yet few studies have examined the environmental dependence of aging patterns across the entire life span. We do so, using a 20‐yr longitudinal data set of reproductive phenotypes in long‐lived female Nazca boobies (Sula granti), a monogamous seabird breeding in the eastern tropical Pacific. Young and old females may suffer from inexperience and senescence, respectively, and/or practice reproductive restraint. Breeding performance (for breeding participation, breeding date, clutch size, egg volume, and offspring production) was expected to be lower in these age classes, particularly under environmental challenge, in comparison with middle‐aged breeders. Sea surface temperature anomalies (SSTA) represented interannual variation in the El Niño–Southern Oscillation (ENSO) and were one proxy for environmental quality (a population count of clutch initiations was a second). Although only females lay eggs, both sexes care for eggs and nestlings, and the male partner’s age, alone or in interaction with female age, was evaluated as a predictor of breeding performance. Middle‐aged females performed better than young and old birds for all reproductive traits. Pairing with a young male delayed breeding (particularly for old females) and reduced clutch size, and pairing with an old male reduced offspring production. Challenging environments increased age effects on breeding probability and breeding date across young to middle ages and for offspring production across middle to old ages. However, important exceptions to the predicted patterns for clutch size and fledging success across young to middle ages suggested that trade‐offs between fitness components may complicate patterns of trait expression across the life span. Relationships between breeding participation, environment, and individual quality and/or experience in young females may also contribute to unexpected patterns for clutch size and fledging success, traits expressed only in breeders. Finally, independent of age, breeding responses of female Nazca boobies to the ENSO did not follow expectations derived from oceanic forcing of primary productivity. During El Niño‐like conditions, egg‐laying traits (clutch size, breeding date) improved, but offspring production declined, whereas La Niña‐like conditions were “poor” environments throughout the breeding cycle.

    more » « less