Roots are crucial for nutrient and water acquisition and can be targeted to enhance plant productivity under a broad range of growing conditions. A current challenge for plant breeding is the limited ability to phenotype and select for desirable root characteristics due to their underground location. Plant breeding efforts aimed at modifying root traits can result in novel, more stress-tolerant crops and increased yield by enhancing the capacity of the plant for soil exploration and, thus, water and nutrient acquisition. Available approaches for root phenotyping in laboratory, greenhouse and field encompass simple agar plates to labor-intensive root digging (i.e., shovelomics) and soil boring methods, the construction of underground root observation stations and sophisticated computer-assisted root imaging. Here, we summarize root architectural traits relevant to crop productivity, survey root phenotyping strategies and describe their advantages, limitations and practical value for crop and forage breeding programs.

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SUMMARYSystems analysis of two alfalfa varieties, Wisfal (Medicago sativa ssp. falcata var. Wisfal) and Chilean (M. sativa ssp. sativa var. Chilean), with contrasting tolerance/sensitivity to drought revealed common and divergent responses to drought stress. At a qualitative level, molecular, biochemical, and physiological responses to drought stress were similar in the two varieties, indicating that they employ the same strategies to cope with drought. However, quantitative differences in responses at all levels were revealed that may contribute to greater drought tolerance in Wisfal. These included lower stomatal density and conductance in Wisfal; delayed leaf senescence compared with Chilean; greater root growth following a drought episode, and greater accumulation of osmolytes, including raffinose and galactinol, and flavonoid antioxidants in roots and/or shoots of Wisfal. Genes encoding transcription factors and other regulatory proteins, and genes involved in the biosynthesis of osmolytes and (iso)flavonoids were differentially regulated between the two varieties and represent potential targets for improving drought tolerance in alfalfa in the future.

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi Syd., is a widespread disease of soybean [Glycine max (L.) Merr.] with the potential to cause serious economic losses. The objective of this study was to genetically map red‐brown lesion type resistance from the cultivar Hyuuga. A population of 117 recombinant inbred lines (RILs) from the cross of Dillon (tan lesion) × Hyuuga (red‐brown [RB] lesion) was rated for ASR lesion type in the field and inoculated with P. pachyrhizi in the greenhouse. The RB resistance gene mapped between Satt460 and Satt307 on linkage group (LG)‐C2. When field severity and lesion density in the greenhouse were mapped, the Rpp?(Hyuuga) locus explained 22 and 15% of the variation, respectively (P < 0.0001). The RB lesion type was associated with lower severity, fewer lesions, and reduced sporulation when compared to the tan lesion type. A population from the cross of Benning × Hyuuga was screened with simple sequence repeat (SSR) markers in the region on LG‐C2 flanked by Satt134 and Satt460. Genotype at these markers was used to predict lesion type when the plants were exposed to P. pachyrhizi All the lines selected for the Hyuuga markers in this interval had the RB lesion type and they averaged approximately 50% fewer lesions compared to lines with tan lesions. Sporulation was only detected in 6% of the RB lines compared with 100% of the tan lines. Marker‐assisted selection can be used to develop soybean cultivars with the Rpp?(Hyuuga) gene for resistance to ASR.

Large portions of the world's arable acreage experience water stress on a regular basis. Improving crop productivity in such drought‐prone environments is a critical breeding objective. The goal of this study was to detect quantitative trait loci (QTL) associated with alfalfa (Medicago sativa L.) forage productivity during drought stress. Two first‐generation backcross (BC1) mapping populations (n = 253) derived from a cross between M. sativa subsp. sativa and M. sativa subsp. falcata were used to develop an updated tetraploid (2n = 4x = 32) genetic linkage map constructed from 600 single‐dose allele molecular markers. Map lengths associated with the two populations were 1293 and 1049 cM, with an average marker density of 3.8 and 3.9 cM, respectively. Half‐sib families derived from 206 BC1 individuals were evaluated for forage yield in seeded plots in seven water‐stressed environments in New Mexico and Oklahoma, USA. Significant genotype effects were detected within each population and environment. Interval mapping analysis identified 10 and 15 QTL that, respectively, improved or reduced forage yield during drought. Average phenotypic effects of each QTL on biomass yield ranged from 3 to 6% and the direction of these effects were generally consistent over environments. Desirable alleles identified in these parents may be suitable for marker‐aided introgression into elite populations to incrementally improve their forage productivity in water‐limited environments.